Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Problems with dbSNP file using the HaplotypeCaller
I am having the following problem:
I use the HaplotypeCaller (GATK 3.3.0) for variant calling. To identify variants that are known according to dbSNP, I use the "--dbsnp" statement and define a dbSNP file (vcf file). I thought, that everything would work fine, but by coincidence I observed a (in my eyes really serious) problem: The same call is recognized in the case of one sample, but not in the case of another sample. These are the two important lines of the vcf files that get reported:
17 7579643 . CCCCCAGCCCTCCAGGT C 5066.73 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=4.819;ClippingRankSum=-1.054;DP=231;FS=78.565;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;MQRankSum=-0.994;QD=21.93;ReadPosRankSum=-5.473;SOR=1.639;set=variant;EFF=INTRON(MODIFIER||||393|TP53|protein_coding|CODING|ENST00000445888|3|1) GT:AD:DP:GQ:PL 1/1:23,207:230:99:5104,251,0
17 7579643 rs59758982 CCCCCAGCCCTCCAGGT C 2868.73 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=3.120;ClippingRankSum=0.256;DB;DP=134;FS=1.120;MLEAC=2;MLEAF=1.00;MQ=59.91;MQ0=0;MQRankSum=1.849;QD=21.41;ReadPosRankSum=-1.285;SOR=0.704;set=variant;EFF=INTRON(MODIFIER||||393|TP53|protein_coding|CODING|ENST00000445888|3|1) GT:AD:DP:GQ:PL 1/1:13,121:134:96:2906,96,0
As we exclude known variants for our analysis, it is essential that this step works correctly. Yet, I am pretty insecure what to do no. The variant seems to be well known (according to information on the ncbi homepage). Yet, why was it not identified in the other sample???
It would be great if anyone could help me. Many thanks in advance!