The original code was authored by Oscar Rodriguez: https://github.com/oscarlr/IGenotyper
usage: plot_sv_gene_cov.py [-h] sample_name input_bam phased_reads phased_snps phased_blocks gene_coords sv_coords target_regions
Create IGenotyper reports and statistics
positional arguments:
sample_name - Sample name
input_bam - Input bam file (ccs.bam)
phased_reads - Phased reads file (ccs_to_ref_phased_sorted.bam)
phased_snps - SNPs annotated with phase (1/1, 0|1, 1|0) (phased_snps.vcf)
phased_blocks - Phased blocks (phased_blocks.txt)
gene_coords - Gene coordinates (gene_coords.bed)
sv_coords - SV coords (sv_coords.bed)
target_regions - Target regions (target_regions.bed)
options:
-h, --help - show this help message and exit
Various files will be created in the current directory - see below for notes on input and output files.
input_bam - BAM file of reads produced by the PacBio sequencer.
phased_reads - BAM file of reads phased by IGenotyper, aligned against the reference sequence.
phased_snps - VCF file of phased SNPs in the reads, compared to the reference sequence. By default, IGenotyper produces this via 'whatshap phase'.
phased_blocks - phased block list in TSV format, as produced by 'whatshapp stats --block-list'.
gene_coords - BED file of core coding regions of V(D)J genes.
sv_coords - BED file of structural variants included in the reference. Presence or absence of these in the sample will be highlighted in the plots.
target_regions - BED file of capture-probe target regions. Coverage of these will be highlighted in the plots.
primary.bam - BAM file of reads that are primary alignments in input_bam.
stats.json - selected stats (calculated stats are pushed into this file and report.html via templates)
report.html - composite report bringing together the plots and statistics
ccs_read_lengths.png - histogram of read lengths in input_bam
ccs_read_quals.png - histogram of CCS quality scores in input_bam
gene_cov.png - read coverage in primary.bam of all genes in gene_coords
sv_gene_cov.png - read coverage in primary.bam of all genes in SVs
phasing.png - genome tracks showing phasing, coverage, SVs etc
hap 0,1,2 .bam - haplotyped sets of primary reads, used to produce bigwig coverage plots
phased_snps.bed - SNPs explicitly phased to 0|1 or 1|0, used for coverage plots
unphased_snps.bed - SNPs not explicitly phased to 0|1 or 1|0 (1/1), used for coverage plots
hap 0,1,2,all .bw - coverage plots
gene_cov.txt - file produced for rplot_gene_cov.R listing gene coverage by haplotype
gene_coords.bed, sv_coords.bed - copied to the working directory for use by pygenometracks
Rplots.pdf - intermediate file produced by rplot_gene_cov.R
rplot_gene_cov.R has an explicit list of igh SVs and the genes they contain
There are a number of things that are specific to igh in the plots and statistics - searching for 'igh' finds these, I think