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Allele depth difference between mutect VCF and IGV
Dear Mutect team,
I usually use Mutect for calling somatic mutations. I faced problem with depth in variant position.
We use both paired (tumor- matched normal) and tumor only analysis. For instance, Mutect called somatic mutations as follows:
7 55259445 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:62,9:24:71:0.127:2 0:0,0:.:0:0.00:0
7 55259446 . A T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:63,7:26:70:0.100:2 0:0,0:.:0:0.00:0
These two positions have approximately 70x for total reads and 10% variant allele frequencies in VCF file
However, the total depth and variant allele depth in those position were 200x and 100x (50%) in IGV.
Please let me know why VCF present quite less read depth than IGV. Are there any reads filtering steps for calling variants?
I have one more question. If there are overlapped reads that are originated from insert size ( e.g) 250bp - insert size, 150 bp * 2 - sequencing read), how does Mutect treat the reads?