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HaplotypeCaller --dbsnp

blueskypyblueskypy Posts: 194Member
edited June 2013 in Ask the GATK team

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?

Post edited by blueskypy on
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