Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Selectvariants for SNPs selection produces .vcf file without homozygous-REF calls

0

5 comments

  • Avatar
    Pamela Bretscher

    Hi Amod Kumar,

    When running GenotypeGVCFs, you can include the --include-non-variant-sites argument to keep your non-variant calls in your VCF prior to filtering. Is this helpful?

    Kind regards,

    Pamela

    0
    Comment actions Permalink
  • Avatar
    Amod Kumar

    Thank you Pamela for this suggestion. I generated .vcf file using GenotypeGVCFs, using  --include-non-variant-sites. When I tried to separate SNPs using  --SelectVariants, the output .vcf file did not have homozygous-REF calls. I want to generate .vcf file with SNPs (no InDels) and homozygous-REF calls.

    Regards

    Amod

    0
    Comment actions Permalink
  • Avatar
    Pamela Bretscher

    Hi Amod Kumar,

    I believe this is an expected result because the homozygous reference calls are not viewed as SNPs so they would be filtered out when you select for SNPs. You may be able to get the results you're looking for by using --select-type-to-exclude to exclude indels in SelectVariants rather than selecting for SNPs. 

    Kind regards,

    Pamela

    0
    Comment actions Permalink
  • Avatar
    Amod Kumar

    Thank you Pamela for your kind suggestion. It worked for me.

    Regards

    Amod

    0
    Comment actions Permalink
  • Avatar
    Pamela Bretscher

    Hi Amod Kumar, great! I'm glad to hear it's working for you now.

    0
    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk