HaplotypeCaller --dbsnp
Posted in Ask the GATK team | Last updated on 2013-06-14 18:31:04

Comments (4)

The doc says "dbSNP is not used in any way for the calculations themselves. --dbsnp binds reference ordered data". Does it mean that the determination of whether a locus is a variant is not influenced by whether that variant is present at dbSNP? what does "--dbsnp binds reference ordered data" mean?

Also why isn't there a --indel option?

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