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Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
Known sites for indel realignment and BQSR in hg38 bundle
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?