I use Mutect2 -tumor only with PON generated with 30 samples; the origin of the samples has the following features:
-Panel of 143 genes
-Average depth of 1200x
-sequencing system Hiseq 2500 for a 125 base paired-end
-sample of peripheral blood
Both versions (gatk 220.127.116.11 and 18.104.22.168) were tested but there is no match in the depth of the reported variants and IGV.
In addition to this, the parameter -- max - reads -per- alignment - start was disabled to see if there was a greater coincidence in the reported depths.
The results showed too much discrepancy in what was reported by Mutect2 and IGV; added to this the total of variants found between the versions doesn´t match.
I understand that there are differences between DP, AD, and IGV but my results seem spurious.
b) Exact command used:
gatk Mutect2 -R ucsc.hg19.fasta -I x.bam -tumor x.bam --germline-resource af-only-gnomad.raw.sites.hg19.vcf.gz --af-of-alleles-not-in-resource 0.0000025 -L xxx.interval_list --panel-of-normals PoN.vcf.gz -O xx.vcf.gz
gatk Mutect2 -R ucsc.hg19.fasta -I x.bam -tumor x.bam --germline-resource af-only-gnomad.raw.sites.hg19.vcf.gz --af-of-alleles-not-in-resource 0.0000025 --max-reads-per-alignment-start 0 -L xxx.interval_list --panel-of-normals PoN.vcf.gz -O xx.vcf.gz-
-max read per alignment start 50 :
Please sign in to leave a comment.