Known sites for indel realignment and BQSR in hg38 bundle

SvyatoslavSidorovSvyatoslavSidorov St. Petersburg, RussiaMember
in Ask the GATK team

Dear GATK team,

I'd like to learn what files I should use for indel realignment and BQSR from hg38 bundle? (I read the manual on this topic -- https://broadinstitute.org/gatk/guide/article?id=1247 -- but just would like to be sure):

1) Am I right that for indel realignment I should use Mills_and_1000G_gold_standard.indels.hg38.vcf and 1000G_phase1.snps.high_confidence.hg38.vcf.gz ?

2) Am I right that for BQSR I should use Mills_and_1000G_gold_standard.indels.hg38.vcf , 1000G_phase1.snps.high_confidence.hg38.vcf.gz , and dbsnp_144.hg38.vcf ?

3) Are there any other files with known sites I should use for indel realignment and BQSR?

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  • SvyatoslavSidorovSvyatoslavSidorov St. Petersburg, RussiaMember

    Dear Sheila, thank you for your quick reply!

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  • NandaNanda CanadaMember

    Dear Sheila and Svyatoslav,

    I have a doubt here, Svyatoslav is looking for indel realignment. As per his question, he mentioned that to use following vcf files
    1) Mills_and_1000G_gold_standard.indels.hg38.vcf
    2) 1000G_phase1.snps.high_confidence.hg38.vcf

    But the 2nd file is not for indels. It looks like it has 1000G_phase1 high confidence SNPS. Am I missing some thing here?

    Thanks in advance.

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  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @Nanda
    Hi,

    I think there is some confusion with the naming, and we also need to update the article to refer to hg38 resources. The 1000G_phase1.snps.high_confidence.hg38.vcf will also contain some indels that are useful for Indel Realignment.

    Please also note, it is no longer necessary to run Indel Realignment step. Have a look at this blog post.

    -Sheila

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