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Can we use the last dbSNP build 142 on hg19 with GATK 3.4 ?

jpvjpv franceMember


The question is in the title.
Is there an another recommended build of dbSNP to use with last version on GATK on hg19 ?

Thanks :)


Best Answer


  • jpvjpv franceMember
    edited May 2015

    Yet it seems there is still some incompatibilities. (there is certainly a solution but i don't know it for instance ) My reference file follows the hg19 conventions and the VCF file for snp build 142 follows the b37 conventions. Is there something to do to adapt this ? I know how to sort my vcf according to a reference .dict file but you handle the contig annotation name difference?

    ERROR MESSAGE: Input files /Users/galaxy_dev_user/variant-calling-pipeline-dev/refData/dbSNP/B142/All_20150415.vcf and reference have incompatible contigs: No overlapping contigs found. ERROR /Users/galaxy_dev_user/variant-calling-pipeline-dev/refData/dbSNP/B142/All_20150415.vcf contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT] ERROR reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM]

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Alright, I should have said more explicitly "... any version of dbsnp you want as long as it is derived from the same reference build as the rest of your data & resources".

    Assuming you already have your data aligned to hg19, the simplest thing to do is to get the hg19 version of the dbsnp file. We provide several versions of dbsnp in our resource bundle but off the top of my head I don't think we have 142. If you can't find it anywhere else (which would surprise me), you'll need to liftover the file. See this article for more details.

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