We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
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.
Alternate allele filtering?
I am trying to call Het as: Ref allele 10-90% or Alt allele 10-90. I have four samples. If one sample is Het, that location is preserved if criteria for Het (as earlier) and Homozygous (> 90% of Alt or Ref allele) at other three locations are met. Is there any simple way to achieve this?
I was just trying SelectVariants to filter with these criteria and tried to see if things works. I used <5% alternate allele for first sample and still can see locations with > 5% alt allele. Here are the code and output. please let me know if I am doing wrong? Thanks
$java -jar $gatk -T SelectVariants -R 8771mapped_Pcap_211contigs.fasta -V snps_after_hardFilter_20x.vcf -o snps_after_hardFilter_20x_alt10_allHet.vcf -select 'vc.getGenotype("7290_R1").getAD().1 / vc.getGenotype("7290_R1").getDP() < 0.05'
I got alt allele of 23/92 = 0.25
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 7290_R1 7291_R1 8566_R1 8771_R1 2 2212 . G A 592.90 PASSS AC=2;AF=0.250;AN=8;BaseQRankSum=0.845;ClippingRankSum=0.000;DP=257;ExcessHet=3.6798;FS=0.000;ML EAC=2;MLEAF=0.250;MQ=60.00;MQRankSum=0.000;QD=4.94;ReadPosRankSum=-2.023;SOR=0.687 GT:AD:DP:GQ:PL 0/1:69,23:92:99:518,0,2196 0/1:21,7:28:99:109,0,533 0/0:43,0:43:99:0,129,1439 0/0:91,2:93:99:0,223,2719