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.
Please help me to interpret this line. How come I have this disease?
chr1 53676448 . G A 1495.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.48;ClippingRankSum=-5.270e-01;DP=79;ExcessHet=3.0103;FS=4.485;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.775;QD=19.18;ReadPosRankSum=0.403;SOR=0.581;set=variant2 GT:AD:DP:GQ:PL:CGIANN_VARNAME:CGIANN_1000GAF:CGIANN_ESP6500AF 0/1:29,49:78:99:1524,0,780:-,NM_000098.2(CPT2) c.1102G>A (p.V368I):-,0.5:-,0.456405
chr1 53676986 . C . . . END=53678942;NT GT ./.
chr1 53679264 . T . . . END=53680317;NT GT ./.
chr1 53680529 . a . . . END=53681541;NT GT ./.
chr1 53681771 . G . . . END=53682332;NT GT ./.
chr1 53682540 . G . . . END=53683699;NT GT ./.
I only saw one mutation with quite some information, and several other lines without information. How come I have a cpt-2 deficiency?