Which VCF's to use for BQSR in GATK
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Entering edit mode
4.4 years ago

Hi All!

I have the following VCF files downloaded from GATk resource Bundle.

1000G_omni2.5.hg38.vcf
1000G_phase1.snps.high_confidence.hg38.vcf
1000G.phase3.integrated.sites_only.no_MATCHED_REV.hg38.vcf
Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf
hapmap_3.3.hg38.vcf
Homo_sapiens_assembly38.dbsnp138.vcf
Homo_sapiens_assembly38.known_indels.vcf
Mills_and_1000G_gold_standard.indels.hg38.vcf

Should I use all the VCF's for BQSR? Is one VCF for SNP and one for indels sufficient? Is using all VCFs recommended? Why not?

GATK BQSR next-gen-sequencing • 1.8k views
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Entering edit mode
3.5 years ago
kanika.151 ▴ 130
  1. Homo_sapiens_assembly38.dbsnp138.vcf
  2. Homo_sapiens_assembly38.known_indels.vcf
  3. Mills_and_1000G_gold_standard.indels.hg38.vcf

Should be enough. :)

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