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Haplotype Caller on SOLID samples reports less coverage per variant compared to --bamoutput
I'm using the whole GATK workflow to analyze Target Resequencing data coming from SOLID platforms. I followed the Best Practices for analysis and used the proper SOLID flags when using BaseRecalibrator (--solid_recal_mode SET_Q_ZERO_BASE_N --solid_nocall_strategy PURGE_READ), however, when looking at the VCF files after Haplotype Caller something does not add up.
I checked some of the variants inside some of my samples and i found that the DP field does not report the same per base coverage value than the one that are reported by the bam (using the --bamOutput to produce a bam for Haplotype Caller) when looking at them using the IGV. As far as I understand, for each position there's a downsampling, but I'm see a lower DP value compared to the ones that are stored in the BAM
I'm attaching an IGV screenshots of one of the variants in which i'm encountering this problem. I deactivated all filtering alignment options in IGV, as well as downsampling. Here's the line Reported in the VCF for this variant:
chr17 45249306 rs62077265 T C 11069.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.010;ClippingRankSum=-0.616;DB;DP=375;FS=90.048;MLEAC=1;MLEAF=0.500;MQ=59.56;MQRankSum=1.319;QD=29.52;ReadPosRankSum=2.229;SOR=0.016 GT:AD:DP:GQ:PL 0/1:150,224:374:99:11098,0,5080
As you can see from the screenshot, not only the covers differ, but a lot of reads that maps according to the reference are missing-
Does somebody has an idea of what happened to the coverage inside the VCF?
Thanks a lot for your time!