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.
Notice:
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.
Attention:
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!

Can a SNP with 35 vs 54 reads really be homozygous?

KubiacKubiac Halle (Saale), GermanyMember

We have sequencing information for a whole family (father, mother, 3 kids) and analyzed them with the gatk (more info below). And while looking through the results I found a SNP with these predicted genotypes and read frequencies:
kid 1: 0/0, 168 vs. 26 reads
mother: 0/0, 211 vs. 34 reads
father: 0/0, 220 vs 18 reads
kid 2: 1/1, 35 vs. 54 reads
kid 3: 1/1, 20 vs. 42 reads

First it caught my eye because of the impossible heredity but than I also noticed the, at least to me, strange genotype calls for kid 2 and 3. Can you explain the effects that lead to such results?

Thank you
Martin

exact vcf entry:
4 71347185 . T C 332.95 . AC=4;AF=0.400;AN=10;BaseQRankSum=3.959;DP=828;Dels=0.00;FS=0.000;HaplotypeScore=11.5830;MLEAC=4;MLEAF=0.400;MQ=29.13;MQ0=153;MQRankSum=-6.418;QD=2.20;ReadPosRankSum=-10.775;SOR=0.708 GT:AD:DP:GQ:PL 0/0:168,26:194:99:0,157,2194 0/0:211,34:245:93:0,93,2661 0/0:220,18:238:99:0,101,2422 1/1:35,54:89:15:131,15,0 1/1:20,42:62:27:250,27,0

pipeline (not all under my control):

  • mapper is unknown, probably bwa
  • Picard MarkDuplicates (Version 1.128)
  • GATK IndelRealigner (Version unknown)
  • GATK UnifiedGenotyper (Version 3.4-46), I know it is deprecated but we had to use it for a reason

Best Answer

Answers

Sign In or Register to comment.