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

SelectVariants to get a vcf file with 1 individual from a vcf file with 3 individuals



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    Hi Linda Do

    Such simple tasks do not require such complex solutions. There is a BCFtools package for any manipulations with VCF files. All you have to do is to run

    bcftools view -O v -o <output_vcf_file> -s <sample_name> <input_vcf_file> 

    The sample names in your VCF are 10017333.1_CS-64, 10017333.1_CS-65 and 10017333.1_CS-66. You have to know which one corresponds to a child.


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    Linda Do

    Thank you so much!


    I used:

    bcftools view -O v -o CS64.vcf -s 10017333.1_CS-64 craSyn-Trio2.recode.vcf

    And it worked!
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    Hi Linda Do,

    The only problem with your code was that you forgot to put a "-" before sn, like this "-sn".

    Just in case anyone else stumbles on this :)


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