Could any one please tell me what is the role of the dbsnp vcf file in the GATK Base Quality Score recalibration program -> http://www.broadinstitute.org/gsa/wi..._recalibration
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Originally posted by nickloman View PostIt's to mask out known SNPs so those positions don't get counted as mismatches / sequence errors.
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Have a dig around here
and
Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk repository - File not found · broadgsa/gatk
Similar SNPs or the same SNP? I don't think the presence of the same SNP would make any difference to the result, the call is either ignored or it isn't.
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Originally posted by nickloman View PostHave a dig around here
and
Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk repository - File not found · broadgsa/gatk
Similar SNPs or the same SNP? I don't think the presence of the same SNP would make any difference to the result, the call is either ignored or it isn't.
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