Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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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

MakeSitesOnlyVCF deletes the most of the variants from cohort vcf


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    Gökalp Çelik

    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.


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