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##########################################################################
## Comparison between TinDaisy_vs_SomaticWrapper ##
## Last modified: 08/29/2022 ##
## Contact: Yizhe Song (y.song@wustl.edu); ##
## Xiangyu Chen ##
## Matthew Wyczalkowski (m.wyczalkowski@wustl.edu) ##
##########################################################################
Case Type Tindaisy Somatic Wrapper
ALCH-ADU4 FF ALCH-ADU4_FF_Tindaisy_HotspotFiltered.vcf ALCH-ADU4_FF_SomaticWrapper_HotspotFiltered.vcf
ALCH-ADU4 FFPE ALCH-ADU4_FFPE_Tindaisy_HotspotFiltered.vcf ALCH-ADU4_FFPE_SomaticWrapper_HotspotFiltered.vcf
ALCH-ADX0 FF ALCH-ADX0_FF_Tindaisy_HotspotFiltered.vcf ALCH-ADX0_FF_SomaticWrapper_HotspotFiltered.vcf
ALCH-ADX0 FFPE ALCH-ADX0_FFPE_Tindaisy_HotspotFiltered.vcf ALCH-ADX0_FFPE_SomaticWrapper_HotspotFiltered.vcf
ALCH-AD8B FF ALCH-AD8B_FF_Tindaisy_HotspotFiltered.vcf ALCH-AD8B_FF_SomaticWrapper_HotspotFiltered.vcf
ALCH-AD8B FFPE ALCH-AD8B_FFPE_Tindaisy_HotspotFiltered.vcf ALCH-AD8B_FFPE_SomaticWrapper_HotspotFiltered.vcf
ALCH-AF1Y FF ALCH-AF1Y_FF_Tindaisy_HotspotFiltered.vcf ALCH-AF1Y_FF_SomaticWrapper_HotspotFiltered.vcf
ALCH-AF1Y FFPE ALCH-AF1Y_FFPE_Tindaisy_HotspotFiltered.vcf ALCH-AF1Y_FFPE_SomaticWrapper_HotspotFiltered.vcf
Case Type Tindaisy rename_file_name Somatic Wrapper rename_file_name
ALCH-ADU4 FF /storage1/fs1/dinglab/Active/Projects/chen.xiangyu/cromwell-data/cromwell-workdir/cromwell-executions/tindaisy2.6.1.cwl/0bbcaaed-00cd-4bb3-8f5d-9c2587f97ef8/call-canonical_filter/execution/output/HotspotFiltered.vcf ALCH-ADU4_FF_Tindaisy_HotspotFiltered.vcf /storage1/fs1/dinglab/Active/Projects/chen.xiangyu/Alchemist/maf_data/data/ALCH-ADU4/FF/ALCH-ADU4-TTP1-A_T.vcf ALCH-ADU4_FF_SomaticWrapper_HotspotFiltered.vcf
ALCH-ADU4 FFPE /storage1/fs1/dinglab/Active/Projects/chen.xiangyu/cromwell-data/cromwell-workdir/cromwell-executions/tindaisy2.6.1.cwl/439383b7-3abb-4a26-b24e-a9b2c734f32d/call-canonical_filter/execution/output/HotspotFiltered.vcf ALCH-ADU4_FFPE_Tindaisy_HotspotFiltered.vcf /storage1/fs1/dinglab/Active/Projects/chen.xiangyu/Alchemist/maf_data/data/ALCH-ADU4/FFPE/ALCH-ADU4-TTR1-A_T.vcf ALCH-ADU4_FFPE_SomaticWrapper_HotspotFiltered.vcf
ALCH-ADX0 FF /storage1/fs1/dinglab/Active/Projects/chen.xiangyu/cromwell-data/cromwell-workdir/cromwell-executions/tindaisy2.6.1.cwl/dd656d1a-60d5-4923-b438-9482f80abe77/call-canonical_filter/execution/output/HotspotFiltered.vcf ALCH-ADX0_FF_Tindaisy_HotspotFiltered.vcf /storage1/fs1/dinglab/Active/Projects/chen.xiangyu/Alchemist/maf_data/data/ALCH-ADX0/FF/ALCH-ADX0-TTP1-A_T.vcf ALCH-ADX0_FF_SomaticWrapper_HotspotFiltered.vcf
ALCH-ADX0 FFPE /storage1/fs1/dinglab/Active/Projects/chen.xiangyu/cromwell-data/cromwell-workdir/cromwell-executions/tindaisy2.6.1.cwl/cb9824e2-ec19-4bc2-b7d0-f87f1584ab14/call-canonical_filter/execution/output/HotspotFiltered.vcf ALCH-ADX0_FFPE_Tindaisy_HotspotFiltered.vcf /storage1/fs1/dinglab/Active/Projects/chen.xiangyu/Alchemist/maf_data/data/ALCH-ADX0/FFPE/ALCH-ADX0-TTR1-A_T.vcf ALCH-ADX0_FFPE_SomaticWrapper_HotspotFiltered.vcf
ALCH-AD8B FF /storage1/fs1/dinglab/Active/Projects/chen.xiangyu/cromwell-data/cromwell-workdir/cromwell-executions/tindaisy2.6.1.cwl/1443ca5f-6abe-4583-93be-cbb3d5e78a9e/call-canonical_filter/execution/output/HotspotFiltered.vcf ALCH-AD8B_FF_Tindaisy_HotspotFiltered.vcf /storage1/fs1/dinglab/Active/Projects/chen.xiangyu/Alchemist/maf_data/data/ALCH-AD8B/FF/ALCH-AD8B-TTP1-A_T.vcf ALCH-AD8B_FF_SomaticWrapper_HotspotFiltered.vcf
ALCH-AD8B FFPE /storage1/fs1/dinglab/Active/Projects/chen.xiangyu/cromwell-data/cromwell-workdir/cromwell-executions/tindaisy2.6.1.cwl/a147f970-5cab-4c0b-a948-65f2824f6425/call-canonical_filter/execution/output/HotspotFiltered.vcf ALCH-AD8B_FFPE_Tindaisy_HotspotFiltered.vcf /storage1/fs1/dinglab/Active/Projects/chen.xiangyu/Alchemist/maf_data/data/ALCH-AD8B/FFPE/ALCH-AD8B-TTR1-A_T.vcf ALCH-AD8B_FFPE_SomaticWrapper_HotspotFiltered.vcf
ALCH-AF1Y FF /storage1/fs1/dinglab/Active/Projects/chen.xiangyu/cromwell-data/cromwell-workdir/cromwell-executions/tindaisy2.6.1.cwl/3ac959fa-c6d6-447a-b13b-6f294b23eb2c/call-canonical_filter/execution/output/HotspotFiltered.vcf ALCH-AF1Y_FF_Tindaisy_HotspotFiltered.vcf /storage1/fs1/dinglab/Active/Projects/chen.xiangyu/Alchemist/maf_data/data/ALCH-AF1Y/FF/ALCH-AF1Y-TTP1-A_T.vcf ALCH-AF1Y_FF_SomaticWrapper_HotspotFiltered.vcf
ALCH-AF1Y FFPE /storage1/fs1/dinglab/Active/Projects/chen.xiangyu/cromwell-data/cromwell-workdir/cromwell-executions/tindaisy2.6.1.cwl/adfd4b80-b983-4a9c-b145-6a2f8a820b5d/call-canonical_filter/execution/output/HotspotFiltered.vcf ALCH-AF1Y_FFPE_Tindaisy_HotspotFiltered.vcf /storage1/fs1/dinglab/Active/Projects/chen.xiangyu/Alchemist/maf_data/data/ALCH-AF1Y/FFPE/ALCH-AF1Y-TTR1-A_T.vcf ALCH-AF1Y_FFPE_SomaticWrapper_HotspotFiltered.vcf
####
cp /storage1/fs1/dinglab/Active/Projects/chen.xiangyu/cromwell-data/cromwell-workdir/cromwell-executions/tindaisy2.6.1.cwl/0bbcaaed-00cd-4bb3-8f5d-9c2587f97ef8/call-canonical_filter/execution/output/HotspotFiltered.vcf /storage1/fs1/dinglab/Active/Projects/ysong/pipelines/vcf_comparison/TinDaisy_vs_SomaticWrapper/TinDaisy_vcf/ALCH-ADU4_FF_Tindaisy_HotspotFiltered.vcf
cp /storage1/fs1/dinglab/Active/Projects/chen.xiangyu/cromwell-data/cromwell-workdir/cromwell-executions/tindaisy2.6.1.cwl/439383b7-3abb-4a26-b24e-a9b2c734f32d/call-canonical_filter/execution/output/HotspotFiltered.vcf /storage1/fs1/dinglab/Active/Projects/ysong/pipelines/vcf_comparison/TinDaisy_vs_SomaticWrapper/TinDaisy_vcf/ALCH-ADU4_FFPE_Tindaisy_HotspotFiltered.vcf
cp /storage1/fs1/dinglab/Active/Projects/chen.xiangyu/cromwell-data/cromwell-workdir/cromwell-executions/tindaisy2.6.1.cwl/dd656d1a-60d5-4923-b438-9482f80abe77/call-canonical_filter/execution/output/HotspotFiltered.vcf /storage1/fs1/dinglab/Active/Projects/ysong/pipelines/vcf_comparison/TinDaisy_vs_SomaticWrapper/TinDaisy_vcf/ALCH-ADX0_FF_Tindaisy_HotspotFiltered.vcf
cp /storage1/fs1/dinglab/Active/Projects/chen.xiangyu/cromwell-data/cromwell-workdir/cromwell-executions/tindaisy2.6.1.cwl/cb9824e2-ec19-4bc2-b7d0-f87f1584ab14/call-canonical_filter/execution/output/HotspotFiltered.vcf /storage1/fs1/dinglab/Active/Projects/ysong/pipelines/vcf_comparison/TinDaisy_vs_SomaticWrapper/TinDaisy_vcf/ALCH-ADX0_FFPE_Tindaisy_HotspotFiltered.vcf
cp /storage1/fs1/dinglab/Active/Projects/chen.xiangyu/cromwell-data/cromwell-workdir/cromwell-executions/tindaisy2.6.1.cwl/1443ca5f-6abe-4583-93be-cbb3d5e78a9e/call-canonical_filter/execution/output/HotspotFiltered.vcf /storage1/fs1/dinglab/Active/Projects/ysong/pipelines/vcf_comparison/TinDaisy_vs_SomaticWrapper/TinDaisy_vcf/ALCH-AD8B_FF_Tindaisy_HotspotFiltered.vcf
cp /storage1/fs1/dinglab/Active/Projects/chen.xiangyu/cromwell-data/cromwell-workdir/cromwell-executions/tindaisy2.6.1.cwl/a147f970-5cab-4c0b-a948-65f2824f6425/call-canonical_filter/execution/output/HotspotFiltered.vcf /storage1/fs1/dinglab/Active/Projects/ysong/pipelines/vcf_comparison/TinDaisy_vs_SomaticWrapper/TinDaisy_vcf/ALCH-AD8B_FFPE_Tindaisy_HotspotFiltered.vcf
cp /storage1/fs1/dinglab/Active/Projects/chen.xiangyu/cromwell-data/cromwell-workdir/cromwell-executions/tindaisy2.6.1.cwl/3ac959fa-c6d6-447a-b13b-6f294b23eb2c/call-canonical_filter/execution/output/HotspotFiltered.vcf /storage1/fs1/dinglab/Active/Projects/ysong/pipelines/vcf_comparison/TinDaisy_vs_SomaticWrapper/TinDaisy_vcf/ALCH-AF1Y_FF_Tindaisy_HotspotFiltered.vcf
cp /storage1/fs1/dinglab/Active/Projects/chen.xiangyu/cromwell-data/cromwell-workdir/cromwell-executions/tindaisy2.6.1.cwl/adfd4b80-b983-4a9c-b145-6a2f8a820b5d/call-canonical_filter/execution/output/HotspotFiltered.vcf /storage1/fs1/dinglab/Active/Projects/ysong/pipelines/vcf_comparison/TinDaisy_vs_SomaticWrapper/TinDaisy_vcf/ALCH-AF1Y_FFPE_Tindaisy_HotspotFiltered.vcf
####
cp /storage1/fs1/dinglab/Active/Projects/chen.xiangyu/Alchemist/maf_data/data/ALCH-ADU4/FF/ALCH-ADU4-TTP1-A_T.vcf /storage1/fs1/dinglab/Active/Projects/ysong/pipelines/vcf_comparison/TinDaisy_vs_SomaticWrapper/Somatic_Wrapper_vcf/ALCH-ADU4_FF_SomaticWrapper_HotspotFiltered.vcf
cp /storage1/fs1/dinglab/Active/Projects/chen.xiangyu/Alchemist/maf_data/data/ALCH-ADU4/FFPE/ALCH-ADU4-TTR1-A_T.vcf /storage1/fs1/dinglab/Active/Projects/ysong/pipelines/vcf_comparison/TinDaisy_vs_SomaticWrapper/Somatic_Wrapper_vcf/ALCH-ADU4_FFPE_SomaticWrapper_HotspotFiltered.vcf
cp /storage1/fs1/dinglab/Active/Projects/chen.xiangyu/Alchemist/maf_data/data/ALCH-ADX0/FF/ALCH-ADX0-TTP1-A_T.vcf /storage1/fs1/dinglab/Active/Projects/ysong/pipelines/vcf_comparison/TinDaisy_vs_SomaticWrapper/Somatic_Wrapper_vcf/ALCH-ADX0_FF_SomaticWrapper_HotspotFiltered.vcf
cp /storage1/fs1/dinglab/Active/Projects/chen.xiangyu/Alchemist/maf_data/data/ALCH-ADX0/FFPE/ALCH-ADX0-TTR1-A_T.vcf /storage1/fs1/dinglab/Active/Projects/ysong/pipelines/vcf_comparison/TinDaisy_vs_SomaticWrapper/Somatic_Wrapper_vcf/ALCH-ADX0_FFPE_SomaticWrapper_HotspotFiltered.vcf
cp /storage1/fs1/dinglab/Active/Projects/chen.xiangyu/Alchemist/maf_data/data/ALCH-AD8B/FF/ALCH-AD8B-TTP1-A_T.vcf /storage1/fs1/dinglab/Active/Projects/ysong/pipelines/vcf_comparison/TinDaisy_vs_SomaticWrapper/Somatic_Wrapper_vcf/ALCH-AD8B_FF_SomaticWrapper_HotspotFiltered.vcf
cp /storage1/fs1/dinglab/Active/Projects/chen.xiangyu/Alchemist/maf_data/data/ALCH-AD8B/FFPE/ALCH-AD8B-TTR1-A_T.vcf /storage1/fs1/dinglab/Active/Projects/ysong/pipelines/vcf_comparison/TinDaisy_vs_SomaticWrapper/Somatic_Wrapper_vcf/ALCH-AD8B_FFPE_SomaticWrapper_HotspotFiltered.vcf
cp /storage1/fs1/dinglab/Active/Projects/chen.xiangyu/Alchemist/maf_data/data/ALCH-AF1Y/FF/ALCH-AF1Y-TTP1-A_T.vcf /storage1/fs1/dinglab/Active/Projects/ysong/pipelines/vcf_comparison/TinDaisy_vs_SomaticWrapper/Somatic_Wrapper_vcf/ALCH-AF1Y_FF_SomaticWrapper_HotspotFiltered.vcf
cp /storage1/fs1/dinglab/Active/Projects/chen.xiangyu/Alchemist/maf_data/data/ALCH-AF1Y/FFPE/ALCH-AF1Y-TTR1-A_T.vcf /storage1/fs1/dinglab/Active/Projects/ysong/pipelines/vcf_comparison/TinDaisy_vs_SomaticWrapper/Somatic_Wrapper_vcf/ALCH-AF1Y_FFPE_SomaticWrapper_HotspotFiltered.vcf
####
scp -r /storage1/fs1/dinglab/Active/Projects/ysong/pipelines/vcf_comparison/TinDaisy_vs_SomaticWrapper/Somatic_Wrapper_vcf/ ysong@katmai.wusm.wustl.edu:/diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/
scp -r /storage1/fs1/dinglab/Active/Projects/ysong/pipelines/vcf_comparison/TinDaisy_vs_SomaticWrapper/TinDaisy_vcf/ ysong@katmai.wusm.wustl.edu:/diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/
## quick overview of the results
1. compare GW/AD_ROI_indel_filtered to TJ Canonical filter yield 2,114 GW unique variants.
2. compare 2,114 GW unique variants to TJ Merge VCF step, yield 2,071 GW unique variants.
3. compare 2,071 GW unique variants to TJ GATK indel bcftool normalize step, yield 2,040 unique GW variants.
4. compare 2,040 unique GW variants to TJ GATK SNP bcftool normalize step, yield 397 unique GW variant. So a larger number of GW unique variants were filtered out at this step. We rescued 1,634 variants here!
5. compare 397 GW unique variants to TJ varscan indel bcftool normalize step, yield 390 unique GW variants.
6. compare 390 GW unique variants to TJ varscan SNP bcftool normalize step, yield 276 unique GW variants.
7. compare 276 unique GW variants to TJ varscan caller, GATK caller and Pindel caller, remain 276 unique GW variants. No variants were rescued in these steps.
For initial testing of the TinJasmine germline variant calling pipeline, we are comparing TinJasmine results with those from GermlineWrapper.
The testing dataset is CPTAC3 LUSC/LSCC sample C3L-00081.
--> GermlineWrapper version:
- Germline variant calling was performed using Song's GermlineWrapper pipeline (https://github.com/ding-lab/germlinewrapper ; latest commit as of 02/04/2019: 8614037).
- Pipeline was slightly modified to work with reference genome GRCh38. Check the following file for changes: /gscmnt/gc2737/ding/fernanda/Germline_MMY/Tools/germlinewrapper_grch38/germlinewrapper.pl
--> CPTAC3 LUSC GermlineWrapper results: /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GermlineWrapper/AD_ROI_indel_filtered/
Directories have the following structure:
/diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GermlineWrapper/AD_ROI_indel_filtered/ # stores germline wrapper results after all filters
/diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/TJ/LUSC/ # stores TinJasmine raw results
/diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/TJ/LUSC/call-canonical_filter/execution/output/ # stores TinJasmine results after canonical filters
## VCF file store the unique GW calls
/diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_Varscan.indel.Final/0000.vcf.gz
##== 1st round of comparisons: sample C3L-00081 ==##
Here, I am comparing the results from GermlineWrapper/AD_ROI_indel_filtered with TinJasmine after the following filters:
* [`GATK_GermlineCaller`](https://github.com/ding-lab/GATK_GermlineCaller.git)
* [`Varscan_GermlineCaller`](https://github.com/ding-lab/Varscan_GermlineCaller.git)
* [`Pindel_GermlineCaller`](https://github.com/ding-lab/Pindel_GermlineCaller.git)
* [`varscan_vcf_remap`](https://github.com/ding-lab/varscan_vcf_remap.git)
* [`MergeFilterVCF`](https://github.com/ding-lab/MergeFilterVCF.git)
* [`TinDaisy-VEP`](https://github.com/ding-lab/TinDaisy-VEP.git)
* [`HotspotFilter`](https://github.com/ding-lab/HotspotFilter.git)
* [`VCF2MAF`](https://github.com/ding-lab/vcf2maf-CWL.git)
* [`VLD_Filter`](https://github.com/ding-lab/VLD_FilterVCF.git)
https://github.com/ding-lab/TinJasmine/blob/master/doc/TinJasmine.wf1.4.png?raw=true
I used bcftools (version 1.14) isec to compare vcf files from the two pipelines.
VCF files must be compressed with bgzip and indexed with tabix prior to using bcftools.
VCF files were also normalized prior to comparison.
Steps taken and summary of results are below.
--> convert vcf.gz file to vcf
cd /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/TinDaisy_vcf
for f in *.vcf.gz; do
gzip -d "$f"
done
cd /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/Somatic_Wrapper_vcf
for f in *.vcf.gz; do
gzip -d "$f"
done
--> VCF normalization:
conda activate sambcf
cd /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/TinDaisy_vcf
for f in *.vcf; do
bcftools norm -f /diskmnt/Projects/Users/ysong/test_data/GRCh38.d1.vd1.fa --multiallelics - --check-ref e -Oz -o "normalized.$f" "$f"
done
cd /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/Somatic_Wrapper_vcf
for f in *.vcf; do
bcftools norm -f /diskmnt/Projects/Users/ysong/test_data/GRCh38.d1.vd1.fa --multiallelics - --check-ref e -Oz -o "normalized.$f" "$f"
done
--> convert vcf file to vcf.gz
cd /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/TinDaisy_vcf
for f in normalized.*.vcf; do
bgzip -c "$f" >"$f.gz"
done
cd /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/Somatic_Wrapper_vcf
for f in normalized.*.vcf; do
bgzip -c "$f" >"$f.gz"
done
--> Indexed resulting vcfs with tabix
cd /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/Somatic_Wrapper_vcf
for f in normalized.*.vcf.gz; do
tabix -p vcf "$f"
done
cd /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/TinDaisy_vcf
for f in normalized.*.vcf.gz; do
tabix -p vcf "$f"
done
--> Compared resulting VCFs:
find /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/ -name "normalized.*.vcf.gz" > /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/Comparison_vcf/vcf.list
cat BCF.list
paste BCF.list | while read BCF ;
do
echo "Processing ""${BCF}""..."
#Create results filename
resultsfile=$(echo "${BCF}" | sed 's/.bcf$//g') ;
echo -e "Results file will be ""${resultsfile}\n" ;
#Add security to ensure that your input files are not overwritten
if [ "${BCF}" == "${resultsfile}" ]
then
echo "Error! - input filename is the same as output file/directory!"
exit 1 ;
fi
bcftools isec Baseline.bcf "${BCF}" -p "${resultsfile}" ;
done ;
cd /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/Comparison_vcf
bcftools isec /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/Somatic_Wrapper_vcf/normalized.ALCH-AD8B_FF_SomaticWrapper_HotspotFiltered.vcf /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/TinDaisy_vcf/normalized.ALCH-AD8B_FF_Tindaisy_HotspotFiltered.vcf -p ALCH-AD8B_FF
######
cd /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/Comparison_vcf
bcftools isec /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/Somatic_Wrapper_vcf/normalized.ALCH-AD8B_FF_SomaticWrapper_HotspotFiltered.vcf.gz /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/TinDaisy_vcf/normalized.ALCH-AD8B_FF_Tindaisy_HotspotFiltered.vcf.gz -p ALCH-AD8B_FF
bcftools isec /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/Somatic_Wrapper_vcf/normalized.ALCH-AD8B_FFPE_SomaticWrapper_HotspotFiltered.vcf.gz /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/TinDaisy_vcf/normalized.ALCH-AD8B_FFPE_Tindaisy_HotspotFiltered.vcf.gz -p ALCH-AD8B_FFPE
bcftools isec /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/Somatic_Wrapper_vcf/normalized.ALCH-ADU4_FF_SomaticWrapper_HotspotFiltered.vcf.gz /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/TinDaisy_vcf/normalized.ALCH-ADU4_FF_Tindaisy_HotspotFiltered.vcf.gz -p ALCH-ADU4_FF
bcftools isec /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/Somatic_Wrapper_vcf/normalized.ALCH-ADU4_FFPE_SomaticWrapper_HotspotFiltered.vcf.gz /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/TinDaisy_vcf/normalized.ALCH-ADU4_FFPE_Tindaisy_HotspotFiltered.vcf.gz -p ALCH-ADU4_FFPE
bcftools isec /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/Somatic_Wrapper_vcf/normalized.ALCH-ADX0_FF_SomaticWrapper_HotspotFiltered.vcf.gz /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/TinDaisy_vcf/normalized.ALCH-ADX0_FF_Tindaisy_HotspotFiltered.vcf.gz -p ALCH-ADX0_FF
bcftools isec /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/Somatic_Wrapper_vcf/normalized.ALCH-ADX0_FFPE_SomaticWrapper_HotspotFiltered.vcf.gz /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/TinDaisy_vcf/normalized.ALCH-ADX0_FFPE_Tindaisy_HotspotFiltered.vcf.gz -p ALCH-ADX0_FFPE
bcftools isec /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/Somatic_Wrapper_vcf/normalized.ALCH-AF1Y_FF_SomaticWrapper_HotspotFiltered.vcf.gz /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/TinDaisy_vcf/normalized.ALCH-AF1Y_FF_Tindaisy_HotspotFiltered.vcf.gz -p ALCH-AF1Y_FF
bcftools isec /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/Somatic_Wrapper_vcf/normalized.ALCH-AF1Y_FFPE_SomaticWrapper_HotspotFiltered.vcf.gz /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/TinDaisy_vcf/normalized.ALCH-AF1Y_FFPE_Tindaisy_HotspotFiltered.vcf.gz -p ALCH-AF1Y_FFPE
#####
bash /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/Comparison_vcf/step1.sh
bcftools isec /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GermlineWrapper/AD_ROI_indel_filtered/C3L-00081.filtered.ROI.AD.5.noLongIndels.normalized.vcf.gz /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/TJ/LUSC/call-canonical_filter/execution/output/HotspotFiltered.vcf.gz -p GW_vs_TJ/GW_vs_canonical_filter -oo GW_vs_TJ/logs/C3L-00081.GW.TJ.isec.log
Examples:
# Create intersection and complements of two sets saving the output in dir/*
bcftools isec A.vcf.gz B.vcf.gz -p dir
# Filter sites in A and B (but not in C) and create intersection
bcftools isec -e'MAF<0.01' -i'dbSNP=1' -e - A.vcf.gz B.vcf.gz C.vcf.gz -p dir
# Extract and write records from A shared by both A and B using exact allele match
bcftools isec A.vcf.gz B.vcf.gz -p dir -n =2 -w 1
# Extract and write records from C found in A and C but not in B
bcftools isec A.vcf.gz B.vcf.gz C.vcf.gz -p dir -n~101 -w 3
# Extract records private to A or B comparing by position only
bcftools isec A.vcf.gz B.vcf.gz -p dir -n -1 -c all
--> Outputs:
sites unique to GW (GW vs. TJ canonical_filter)
/diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_canonical_filter/0000.vcf
change it to gz format
bgzip /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_canonical_filter/0000.vcf /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_canonical_filter/0000.vcf.gz
index it
tabix -p vcf /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_canonical_filter/0000.vcf.gz
Next step we would compare all other TJ steps with this file, to see whether we could rescure these variants.
0000.vcf 0001.vcf 0002.vcf 0003.vcf README.txt sites.txt
SW_vs_TD//0000.vcf for records private to /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/Somatic_Wrapper_vcf/ALCH-AF1Y_FFPE_SomaticWrapper_HotspotFiltered.vcf.gz
SW_vs_TD//0001.vcf for records private to /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/TinDaisy_vcf/ALCH-AF1Y_FFPE_Tindaisy_HotspotFiltered.vcf.gz
SW_vs_TD//0002.vcf for records from /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/Somatic_Wrapper_vcf/ALCH-AF1Y_FFPE_SomaticWrapper_HotspotFiltered.vcf.gz shared by both /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/Somatic_Wrapper_vcf/ALCH-AF1Y_FFPE_SomaticWrapper_HotspotFiltered.vcf.gz /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/TinDaisy_vcf/ALCH-AF1Y_FFPE_Tindaisy_HotspotFiltered.vcf.gz
SW_vs_TD//0003.vcf for records from /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/TinDaisy_vcf/ALCH-AF1Y_FFPE_Tindaisy_HotspotFiltered.vcf.gz shared by both /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/Somatic_Wrapper_vcf/ALCH-AF1Y_FFPE_SomaticWrapper_HotspotFiltered.vcf.gz /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/TinDaisy_vcf/ALCH-AF1Y_FFPE_Tindaisy_HotspotFiltered.vcf.gz
count variants
gatk CountVariants -V /SW_vs_TD/0000.vcf
gatk CountVariants -V /SW_vs_TD/0001.vcf
gatk CountVariants -V /SW_vs_TD/0003.vcf
gatk CountVariants -V /SW_vs_TD/0004.vcf
/diskmnt/Projects/Users/ysong/program/gatk/gatk-4.2.3.0/gatk CountVariants \
-V /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_canonical_filter/0000.vcf.gz
- NUMBER OF VARIANTS UNIQUE TO GERMLINEWRAPPER: 2114
--> convert vcf file to vcf.gz
for f in /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/Comparison_vcf/*/*.vcf; do
bgzip "$f"
done
--> Indexed resulting vcfs with tabix
for f in /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/Comparison_vcf/*/*.vcf.gz; do
tabix -p vcf "$f"
done
for f in /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/Comparison_vcf/*/*.vcf.gz; do
bcftools stats "$f" >"$f.file.stats"
done
for f in /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/Comparison_vcf/*/*.vcf; do
bcftools stats "$f" >"$f.file.stats"
done
#####
cd /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/Comparison_vcf/*/
for f in /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/Comparison_vcf/*/*.vcf.gz; do
/diskmnt/Projects/Users/ysong/program/gatk/gatk-4.2.3.0/gatk CountVariants -V "$f" >> "$f_count_variants.txt"
done
for f in /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/Comparison_vcf/*/*.vcf.gz.file.stats; do
cat "$f" >> /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/Comparison_vcf/stats.txt
done
for f in /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/Comparison_vcf/*/*.vcf.file.stats; do
cat "$f" >> /diskmnt/Projects/Users/ysong/project/variant_calling_pipeline/pipeline_comparison/TinDaisy_vs_SomaticWrapper/Comparison_vcf/stats.txt
done
### 1. GW unique from step0 vs mergeVCF
bcftools isec /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_canonical_filter/0000.vcf.gz /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/TJ/LUSC/call-merge_vcf/execution/output/merged.vcf.gz -p GW_vs_TJ/GW_vs_merge_vcf
bgzip /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_merge_vcf/0000.vcf /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_merge_vcf/0000.vcf.gz
tabix -p vcf /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_merge_vcf/0000.vcf.gz
count variants
/diskmnt/Projects/Users/ysong/program/gatk/gatk-4.2.3.0/gatk CountVariants \
-V /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_merge_vcf/0000.vcf.gz
- NUMBER OF VARIANTS UNIQUE TO GERMLINEWRAPPER: 2071
### 2. GW unique from step1 vs bcftools_normalize_gatk_indel
bcftools isec /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_merge_vcf/0000.vcf.gz /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/TJ/LUSC/call-bcftools_normalize_gatk_indel/execution/output.normalized.vcf.gz -p GW_vs_TJ/GW_vs_bcftools_normalize_gatk_indel
"/diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_normalize_gatk_indel/0000.vcf"
bgzip /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_normalize_gatk_indel/0000.vcf /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_normalize_gatk_indel/0000.vcf.gz
tabix -p vcf /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_normalize_gatk_indel/0000.vcf.gz
/diskmnt/Projects/Users/ysong/program/gatk/gatk-4.2.3.0/gatk CountVariants \
-V /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_normalize_gatk_indel/0000.vcf.gz
- NUMBER OF VARIANTS UNIQUE TO GERMLINEWRAPPER: 2040
### 3. GW unique from step2 vs bcftools_normalize_gatk_snp
bcftools isec /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_normalize_gatk_indel/0000.vcf.gz /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/TJ/LUSC/call-bcftools_normalize_gatk_snp/execution/output.normalized.vcf.gz -p GW_vs_TJ/GW_vs_bcftools_normalize_gatk_snp
"/diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_normalize_gatk_snp/0000.vcf"
bgzip /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_normalize_gatk_snp/0000.vcf /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_normalize_gatk_snp/0000.vcf.gz
tabix -p vcf /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_normalize_gatk_snp/0000.vcf.gz
/diskmnt/Projects/Users/ysong/program/gatk/gatk-4.2.3.0/gatk CountVariants \
-V /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_normalize_gatk_snp/0000.vcf.gz
- NUMBER OF VARIANTS UNIQUE TO GERMLINEWRAPPER: 397
### 4. GW unique from step3 vs bcftools_normalize_pindel
bcftools isec /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_normalize_gatk_snp/0000.vcf.gz /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/TJ/LUSC/call-bcftools_normalize_pindel/execution/output.normalized.vcf.gz -p GW_vs_TJ/GW_vs_bcftools_normalize_pindel
0000.vcf.gz is the VCF contains VARIANTS UNIQUE TO GERMLINEWRAPPER(excluded rescued variants from mergeVCF, bcftools_normalize_gatk_indel and bcftools_normalize_gatk_snp stages)
output.normalized.vcf.gz is the bcftools_normalize_pindel VCF
Error message:
#[W::bcf_hdr_check_sanity] PL should be declared as Number=G
"/diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_normalize_gatk_snp/0000.vcf"
bgzip /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_normalize_gatk_snp/0000.vcf /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_normalize_gatk_snp/0000.vcf.gz
tabix -p vcf /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_normalize_gatk_snp/0000.vcf.gz
/diskmnt/Projects/Users/ysong/program/gatk/gatk-4.2.3.0/gatk CountVariants \
-V /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_normalize_gatk_snp/0000.vcf.gz
- NUMBER OF VARIANTS UNIQUE TO GERMLINEWRAPPER: 397
### 5. GW unique from step4 vs bcftools_normalize_varscan_indel
bcftools isec /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_normalize_gatk_snp/0000.vcf.gz /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/TJ/LUSC/call-bcftools_normalize_varscan_indel/execution/output.normalized.vcf.gz -p GW_vs_TJ/GW_vs_bcftools_normalize_varscan_indel
"/diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_normalize_varscan_indel/0000.vcf"
bgzip /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_normalize_varscan_indel/0000.vcf /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_normalize_varscan_indel/0000.vcf.gz
tabix -p vcf /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_normalize_varscan_indel/0000.vcf.gz
/diskmnt/Projects/Users/ysong/program/gatk/gatk-4.2.3.0/gatk CountVariants \
-V /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_normalize_varscan_indel/0000.vcf.gz
- NUMBER OF VARIANTS UNIQUE TO GERMLINEWRAPPER: 390
### 6. GW unique from step5 vs bcftools_normalize_varscan_snp
bcftools isec /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_normalize_varscan_indel/0000.vcf.gz /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/TJ/LUSC/call-bcftools_normalize_varscan_snp/execution/output.normalized.vcf.gz -p GW_vs_TJ/GW_vs_bcftools_normalize_varscan_snp
"/diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_normalize_varscan_snp/0000.vcf"
bgzip /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_normalize_varscan_snp/0000.vcf /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_normalize_varscan_snp/0000.vcf.gz
tabix -p vcf /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_normalize_varscan_snp/0000.vcf.gz
bcftools stats "/diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_normalize_varscan_snp/0000.vcf.gz" > /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_normalize_varscan_snp/0000.file.stats
/diskmnt/Projects/Users/ysong/program/gatk/gatk-4.2.3.0/gatk CountVariants \
-V /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_normalize_varscan_snp/0000.vcf.gz
- NUMBER OF VARIANTS UNIQUE TO GERMLINEWRAPPER: 276
### 7. GW unique from step6 vs bcftools_gatk_germline_caller
bcftools isec /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_normalize_varscan_snp/0000.vcf.gz /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/TJ/LUSC/call-gatk_germline_caller/execution/output/GATK.snp.Final.vcf.gz -p GW_vs_TJ/GW_vs_bcftools_gatk_germline_caller
"/diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_gatk_germline_caller/0000.vcf"
bgzip /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_gatk_germline_caller/0000.vcf /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_gatk_germline_caller/0000.vcf.gz
tabix -p vcf /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_gatk_germline_caller/0000.vcf.gz
bcftools stats /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_gatk_germline_caller/0000.vcf.gz > /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_gatk_germline_caller/0000.file.stats
/diskmnt/Projects/Users/ysong/program/gatk/gatk-4.2.3.0/gatk CountVariants \
-V /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_gatk_germline_caller/0000.vcf.gz
- NUMBER OF VARIANTS UNIQUE TO GERMLINEWRAPPER: 276
### 8. GW unique from step7 vs bcftools_gatk_germline_caller
bcftools isec /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_bcftools_gatk_germline_caller/0000.vcf.gz /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/TJ/LUSC/call-gatk_germline_caller/execution/output/GATK.indel.Final.vcf.gz -p GW_vs_TJ/GW_vs_GATK.indel.Final
"/diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_GATK.indel.Final/0000.vcf"
bgzip /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_GATK.indel.Final/0000.vcf /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_GATK.indel.Final/0000.vcf.gz
tabix -p vcf /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_GATK.indel.Final/0000.vcf.gz
bcftools stats /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_GATK.indel.Final/0000.vcf.gz > /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_GATK.indel.Final/0000.file.stats
/diskmnt/Projects/Users/ysong/program/gatk/gatk-4.2.3.0/gatk CountVariants \
-V /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_GATK.indel.Final/0000.vcf.gz
- NUMBER OF VARIANTS UNIQUE TO GERMLINEWRAPPER: 276
### 9. GW unique from step8 vs bcftools_gatk_germline_caller
bcftools norm -f /diskmnt/Projects/Users/ysong/test_data/GRCh38.d1.vd1.fa --multiallelics - --check-ref e -Oz -o /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/TJ/LUSC/call-pindel_filter/execution/filtered/pindel_sifted.out.CvgVafStrand_pass_normalized.vcf.gz /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/TJ/LUSC/call-pindel_filter/execution/filtered/pindel_sifted.out.CvgVafStrand_pass.vcf.gz
bcftools isec /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_GATK.indel.Final/0000.vcf.gz /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/TJ/LUSC/call-pindel_filter/execution/filtered/pindel_sifted.out.CvgVafStrand_pass_normalized.vcf.gz -p GW_vs_TJ/GW_vs_call-pindel_filter
"/diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_GATK.indel.Final/0000.vcf"
bgzip /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_GATK.indel.Final/0000.vcf /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_GATK.indel.Final/0000.vcf.gz
tabix -p vcf /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_GATK.indel.Final/0000.vcf.gz
tabix -p vcf /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/TJ/LUSC/call-pindel_filter/execution/filtered/pindel_sifted.out.CvgVafStrand_pass_normalized.vcf.gz
bcftools stats /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_GATK.indel.Final/0000.vcf.gz > /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_GATK.indel.Final/0000.file.stats
/diskmnt/Projects/Users/ysong/program/gatk/gatk-4.2.3.0/gatk CountVariants \
-V /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_GATK.indel.Final/0000.vcf.gz
- NUMBER OF VARIANTS UNIQUE TO GERMLINEWRAPPER: 276
### 10. GW unique from step9 vs varscan_germline_caller
bcftools isec /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_GATK.indel.Final/0000.vcf.gz /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/TJ/LUSC/call-varscan_germline_caller/execution/output/Varscan.snp.Final.vcf.gz -p GW_vs_TJ/GW_vs_varscan_germline_caller
"/diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_varscan_germline_caller/0000.vcf"
bgzip /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_varscan_germline_caller/0000.vcf /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_varscan_germline_caller/0000.vcf.gz
tabix -p vcf /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_varscan_germline_caller/0000.vcf.gz
bcftools stats /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_varscan_germline_caller/0000.vcf.gz > /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_varscan_germline_caller/0000.file.stats
/diskmnt/Projects/Users/ysong/program/gatk/gatk-4.2.3.0/gatk CountVariants \
-V /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_varscan_germline_caller/0000.vcf.gz
- NUMBER OF VARIANTS UNIQUE TO GERMLINEWRAPPER: 276
### 11. GW unique from step10 vs Varscan.indel.Final
bcftools isec /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_varscan_germline_caller/0000.vcf.gz /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/TJ/LUSC/call-varscan_germline_caller/execution/output/Varscan.indel.Final.vcf.gz -p GW_vs_TJ/GW_vs_Varscan.indel.Final
"/diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_Varscan.indel.Final/0000.vcf"
bgzip /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_Varscan.indel.Final/0000.vcf /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_Varscan.indel.Final/0000.vcf.gz
tabix -p vcf /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_Varscan.indel.Final/0000.vcf.gz
bcftools stats /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_Varscan.indel.Final/0000.vcf.gz > /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_Varscan.indel.Final/0000.file.stats
/diskmnt/Projects/Users/ysong/program/gatk/gatk-4.2.3.0/gatk CountVariants \
-V /diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_Varscan.indel.Final/0000.vcf.gz
- NUMBER OF VARIANTS UNIQUE TO GERMLINEWRAPPER: 276
## VCF file store the unique GW calls
/diskmnt/Projects/Users/ysong/project/PECGS/GermlineWrapper_vs_TinJasmine/SW/CPTAC/LUSC/C3L-00081/GW_vs_TJ/GW_vs_Varscan.indel.Final/0000.vcf.gz