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

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2 comments

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    Nickier

    Hello! Could you improve a readme file to introduct the resource files?  

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    Ashi

    Hi,

    I am trying to run BaseRecalibrator with my WGS data.

    My ref is hg19 reference. Where can I get SNP and Indel vcf files in hg19 version?

     

    I found b37 version files (below) in google cloud gs://gatk-legacy-bundles, but not for hg19.

    dbsnp_138.b37.vcf

    1000G_phase1.indels.b37.vcf (currently from the 1000 Genomes Phase I indel calls)

    Mills_and_1000G_gold_standard.indels.b37.sites.vcf

     

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