haploplot

Plot haplotype-specific barcode coverage around structural variants (deletions or inversions) from linked-read BAM/CRAM data.

What it does

• Computes unique barcode counts per window for HP1 and HP2.
• Supports deletion spanning-barcode mode and inversion breakpoint-linking mode.
• Accepts one or two samples for comparison.
• Optionally draws a gene annotation track from GFF3 (.gff3, .gz, or .tar.gz).

Requirements

• Python 3
• pysam, numpy, pandas, matplotlib

Quick usage

python haploplot.py -p chr1:100000-200000 -s1 sample1.bam -r chr1:110000-190000 -t del

Two-sample inversion example:

python haploplot.py -p chr1:100000-200000 -s1 sample1.bam -s2 sample2.bam -r chr1:120000-180000 -t inv -f 500

For CRAM input, provide a reference:

python haploplot.py -p chr1:100000-200000 -s1 sample1.cram -r chr1:110000-190000 -t del -ref ref.fa

Key arguments

• -p chr:start-end: plot region (required)
• -s1, -s2: sample BAM/CRAM files (at least one required)
• -r chr:start-end: SV region/breakpoints (optional; enables SV barcode selection)
• -t del|inv: SV mode (del default)
• -w: window size (default 2000)
• -f: flank size for SV barcode detection (default 20000)
• -n T|F: normalize per haplotype
• -gff3: optional gene annotation file
• -ref: optional reference FASTA for CRAM
• -o: output image name (default barcode_hp1_hp2_plot.png)