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which input files for IndelRealigner and BaseRecalibrator?

KinMokKinMok LondonMember

Hi

For input file of known indels in IndelRealigner, I would like to ask what is the pros and cons for using Mills_and_1000G_gold_standard.indels.b37.vcf vs 1000G_phase1.indels.b37.vcf ? Both are available from the resource bundle.

A similar question is which of the above 2 files would you suggest for input for known Indel sites in the BaseRecalibrator? Is it the Mills_and_1000G_gold_standard.indels.b37.vcf as the workflow use gold.standard.indel.vcf?
Which should I choose between dbsnp_138.b37.vcf and 1000G_phase1.snps.high_confidence.b37.vcf for the other known site inputs? Is it dbsnp_138.b37.vcf that contains more variant?

Thanks

Kin

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