Question: Which VCF's to use for BQSR in GATK
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rohitsatyam102 • 200 wrote:
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?