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

How do iquery VCF for specific variants by CHROM and POS

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    Pamela Bretscher

    Hi Alon Ziv,

    Have you looked at the SelectVariants documentation and specific arguments? You should be able to use SelectVariants to query variants from specific chromosomes using the -L option. You can also use arguments like --keep-ids to query specific variants. Please let me know if this does not answer your question or doesn't address the specific use case you are looking for.

    Kind regards,

    Pamela

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    Alon Ziv

    Hi Pamela Bretscher,

    I would love to filter my SNPs by ID but as I checked my file it seems that I did not assign any IDs to them ( I used VariantsToTable and asked for IDs and got a column of dots) ... is there a way to do it?  or, if I need to backtrack my steps, when am I supposed to assign IDs to my SNPS?

    Thanks in advance

    Alon

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    Pamela Bretscher

    Hi Alon Ziv,

    I believe you should be able to use VariantAnnotator to add IDs from a dbSNP file to the SNPs in your VCF which is described in the tool documentation. Please let me know if this is helpful for you.

    Kind regards,

    Pamela

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