If you happen to see a question you know the answer to, please do chime in and help your fellow community members. 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.
A bug in snp results from Haplotyper
I took use Haplotyper to get snp.vcf results.
There 's a snp is strange:
chr2 29448423 . T G 299.77 PASS AC=1;AF=0.500;AN=2;DP=114;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.80;MQ0=0;QD=2.63 GT:AD:GQ:PL 0/1:114,0:99:328,0,13034
Both DP and AD are 114;
Depth of reference is also 114.
Isn't this position 0/0 ?
Is this a bug for Haplotyper ?
I checked bam files and found that there were 119 reads covering this position.
114 for T
5 for G
Why is the information of these 5 reads supporting G missing?
Thank you ~