Where num_plus_strand and num_minus_strand refers to read counts for allele base on the plus strand and minus strand respectively.
I wonder if these two fields can be added to vcf-readcount-annotator's output? For standardization's sake, you can put those data to FORMAT fields ADF and ADR like in the official VCF specs, like the following FORMAT header lines in bcftools:
##FORMAT=<ID=ADF,Number=R,Type=Integer,Description="Allelic depths on the forward strand (high-quality bases)">
##FORMAT=<ID=ADR,Number=R,Type=Integer,Description="Allelic depths on the reverse strand (high-quality bases)">
Many pipelines put filters on allele-specific depths, and the removal of the SAC annotation from GATK4 causes quite a bit of hardship.
The bam-readcount output contains allelic read counts on each strand; the readme file provides the following fields for each allele:
Where
num_plus_strand
andnum_minus_strand
refers to read counts for allelebase
on the plus strand and minus strand respectively.I wonder if these two fields can be added to
vcf-readcount-annotator
's output? For standardization's sake, you can put those data to FORMAT fields ADF and ADR like in the official VCF specs, like the following FORMAT header lines in bcftools:Many pipelines put filters on allele-specific depths, and the removal of the SAC annotation from GATK4 causes quite a bit of hardship.
Thanks in advance!