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genomicsDBimport --merge-input-intervals explanation

Hi GATK team,

We have a bunch of WGS samples and would like to import them in genomicsDBimport before joint genotyping. We are for this project interested in coding sequences. For this we want to use all exon coordinates from Gencode (~220K lines). In genomicsDBimport we saw the parameter --merge-input-intervals explanation

--merge-input-intervals / -merge-input-intervals

Boolean flag to import all data in between intervals. Improves performance using large lists of intervals, as in exome sequencing, especially if GVCF data only exists for specified intervals.

What I understood it's that a interval file as :
chr1 1065 2000
chr1 2010 2250
chr2 500 700
chr2 800 1200

if --merge-input-intervals is set it will consider also regions between all intervals ? so in fact an interval list as :
chr1 1065 2250
chr2 500 1200

Could you clarify ? An other idea would be to execute one instance of genomicsDBimport per chromosome and then filter the VCF based on the interval list using selectVariants.

Thank you

Answers

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    HI @NicoBxl

    if --merge-input-intervals is set it will consider also regions between all intervals ? so in fact an interval list as :
    chr1 1065 2250
    chr2 500 1200

    Yes that is correct.
    Use with --only-output-calls-starting-in-intervals if input GVCFs contain calls outside the specified intervals.

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