Which VCF's to use for BQSR in GATK

Question

[rohitsatyam102]

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?

Answer 1

[kanika.151]

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. :)