hi, I'm new here. I am trying to find germline mutations in a mutiplex_pcr generated NGS data with Haplotypecaller (GATK 4.0.4.0 ). I am confused about that why mutations have much less read depth after variant calling compared with that in input bam. For example:
17 41223094 . T C 947.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-6.201;ClippingRankSum=0.000;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=12.64;ReadPosRankSum=-0.181;SOR=0.572 GT:AD:DP:GQ:PL 0/1:55,55:110:99:1586,0,1853
This is a mutation called by Haplotypecaller, the VCF shows the read depth in this positon is 110, but IGV shows the read depth at this position in Bam is around 1000, what makes this difference?
And I checked that there was no read filtered by HaplotypeCaller .
17:32:41.050 INFO HaplotypeCaller - No reads filtered by: ((((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter) AND GoodCigarReadFilter) AND WellformedReadFilter)
Thanks!