MakeSitesOnlyVCF deletes the most of the variants from cohort vcf

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Rafiga Masmaliyeva

• January 30, 2024 16:22

REQUIRED for all errors and issues:
a) GATK version used: GATK/4.4.0.0

b) Exact command used: 

gatk MakeSitesOnlyVcf -I joint_germline.vcf.gz -O sitesonly.vcf.gz

c) Entire program log: 

I run MakeSitesOnlyVcf for cohort vcf file with more than 16 millions of variants and the output vcf files with sites only contains only small fraction of these variants (35000 variants). Why this happens? How could I prevent this?

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  Gökalp Çelik

  • February 27, 2024 09:57

  Hi Rafiga Masmaliyeva

  This is not the regular behavior of this tool. Can you check exactly how many variants you have in the joint_germline.vcf.gz using the command below?

  bcftools view -H  joint_germline.vcf.gz | wc -l

  Also it is possible that your command might have stopped prematurely due to IO errors or else.  Can you provide us the entire log of the tool? There may be a hidden error message somewhere.

  Regards. 

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