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

Where can I find known variants, training and truth sets, and other resource files? Follow

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    Monete Rajão Gomes

    Hi,

    I have some doubts and I hope anyone could help me.

    I'm trying to run gatk pipeline again (I did before successfully), and I decided to use as known site, dbSNP last release (v153).

    So, I've downloaded this dataset: GCF_000001405.25.gz (and .tbi also), from dbSNP FTP which is a vcf file from dbSNP v153, using GRCh37 as reference.

    As other know sites, I will use Mills and 1000g vcf's available at FTP bundle from Broad Inst.

    I noticed that dbSNP vcf have chrom names like "NC_...", "NT_...". But other vcf's from bundle are named as "chr1", "chr2"... accordingly to UCSC hg19 reference.

    So, my questions are:

    1) Is it recommended simply change chrom names to equivalent ones? Is this correct and recommended, without major problems? Example:

    Change "NC_000001.10" to "chr1"
    Change "NC_000002.11" to "chr2"
    Change "NC_000003.11" to "chr3"
    .....
    Change "NC_012920.1" to "chrM"

    2) What do you think about: download dbSNP v153 in GRCh38 version in order to make the liftover to hg19 (using chain table file from UCSC -- with chrom names from UCSC)? Is this ok?

    3) If none of the above, do you have any advice for me, to deal with it?

    Further, I couldn't find any other website/ftp which I could download dbSNP v153  with UCSC hg19 chrom names.

    I'm trying to find a solution. Hope you could help me.

    Thank you for your time and patience.

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