Heads up:
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.

Reference Homozygous AD problem

Dear GATK team,

I am using GATK 4 and I found curious output in gVCF file.

my command was:

gatk --java-options "-Xmx8G -Djava.io.tmpdir=$PWD/tmp -XX:ParallelGCThreads=$cpu" HaplotypeCaller -R $hg38 -I ${arg%.bam}.recal.bam -ERC BP_RESOLUTION --max-alternate-alleles 1 -O ${arg%.bam}.raw.snps.g.vcf -L $bed --dbsnp $dbsnp

And one of the variants (I found many more) is:

chr17 30237328 . T <NON_REF> . . . GT:AD:DP:GQ:PL 0/0:23,19:42:0:0,0,154

I do not understand AD is 23,19 at this 0/0 site. I would expect result like AD=42,0 (for reference homozygous).

Can anybody explain me how is possible that allelic depth is split to two values if only one allele is appearing? Also in IGV I can see only T are in aligned reads at this site.





Sign In or Register to comment.