GATK version used: v184.108.40.206
I have a series of WES samples and ran the somatic mutation calling pipeline (Mutect2). Next, I took the union of all the reported variants. What I would like to know is the coverage on the REF and ALT allele for each variant and for all samples.
I thought I might be able to do this running VariantAnnotator on the merged VCF. Specifically, for a VCF file where variants from sample A, B and C were merged, I ran the command:
gatk VariantAnnotator -V A_B_C_merged.vcf.gz -I A.bam -I B.bam -I C.bam --output VA_ABC.vcf -A Coverage -A DepthPerAlleleBySample -A ChromosomeCounts
It seems that I only get coverage (and other info) when at least 1 read maps to the ALT allele. This even holds for regions with high coverage.
bcftools query -i 'INFO/DP > 500' -f '%CHROM\t%POS\t%ALT\t%REF\t[%DP\t]\n' VA_ABC.vcf returns:
CHR POS REF ALT A B C
chr1 11668809 G A . . 311
chr1 16625831 A G . . 81
chr1 16628668 T C . 201 .
chr1 16686072 C T 164 . .
chr1 16760342 T G 779 . .
chr1 16930115 A C 274 . .
chr1 21885008 T C 119 . .
chr1 58056429 CTAACT C . . 183
For variants with AC==2 (AC==3) I do see the coverage on both (all 3) the samples.
My question is: How do I get coverage info for all variants, even if all reads map to the REF allele for some samples? Is VariantAnnotator the right tool? Should I use a different settting (I checked, but may have overlooked)? Or is a different tool maybe more appropriate?
Thanks in advance!
Please sign in to leave a comment.