HaplotypeCaller --dbsnp

blueskypyblueskypy Posts: 253Member ✭✭
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

Best Answers


  • blueskypyblueskypy Posts: 253Member ✭✭

    Thanks Geraldine for the explanation! But intuitively, wouldn't the verification of a variant calling by dbSNP increase the confidence level of that calling? If so, why wouldn't we use dbSNP to help to make the decision on that call?

    Also you mean I could also add the following to HaplotypeCaller?

    --dbsnp Mills_and_1000G_gold_standard.indels.b37.vcf --dbsnp 1000G_phase1.indels.b37.vcf

  • blueskypyblueskypy Posts: 253Member ✭✭

    Thanks so much, Geraldine! Have a great weekend!

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