gatk haplotypecaller report a mush lower coverage than seen in alignment
Entering edit mode
12 months ago
mark.rose ▴ 40

Hi All

I trying to use gatk's haplotype caller to call variants on pbmm2 aligned PacBio CCS reads thusly:

gatk HaplotypeCaller --reference ../30L02and17L22.2snps.fa --input m200715_080201_42269_c101526542550000001823318810042135_s1_p0.ccs.bam-vs-25C11and66H02.2snps.sort.bam --output m200715_080201_42269_c101526542550000001823318810042135_s1_p0.ccs.bam-vs-25C11and66H02.2snps.gatk.vcf

one of the variants called, for example, is

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  UnnamedSample
30L02   108     .       C       G       796.03  .       AC=2;AF=1.00;AN=2;DP=18;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.43;SOR=0.914        GT:AD:DP:GQ:PL  1/1:0,18:18:54:810,54,0

My question is that the coverage is shown as DP=18, but when I look at the alignment used for this analysis the coverage at this position is 81. It seems like the haplotypecaller is not using all the available data but may be filtering some out (though the reads here look good). Any ideas whats going on and how I can deal with it?

Much thanks

gatk alignment dp coverage haplotypecaller • 308 views
Entering edit mode

I suggest that you ask on GATK's support forum as well and then post the answer here.


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