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

Follow

Amod Kumar

• December 02, 2021 11:03

I generated SNP.vcf file using --Haplotypecaller, --CombinedGVCF, --GenotypeGVCF, SelectVariants and then Hard filtering. The output file did not have homozygous-REF calls. How can I include these calls in my generated vcf files.

Thanks

0

• 

  Pamela Bretscher

  • December 02, 2021 15:28

  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
• 

  Amod Kumar

  • December 03, 2021 04:47

  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
• 

  Pamela Bretscher

  • December 03, 2021 14:04

  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
• 

  Amod Kumar

  • December 06, 2021 04:24

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

  Regards

  Amod

  0

  Comment actions Permalink
• 

  Pamela Bretscher

  • December 06, 2021 14:23

  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.