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CombineGVCFs and exome: can use `-L` in the target regions ?

lindenblindenb FranceMember ✭✭

Hi the GATK team,

I'm currently combining the GVCFs for ~200 exomes with gatk 3.8.
I splitted my work by chromosome (e.g: -L 'chr1' ) . It's still slow and generates some huge files.

To reduce the size of the final g.vcf file, I wonder if it is safe to only combine the gvcf using the BED (extended +/-1Kb) ( -L "slop1Kb.capture.for.chr1.bed.gz" ) and hence ignoring the variants in the intergenic regions. Would I miss some variants in the GenotypeGvcf phase ? Is it a bad practice ?

Thanks in advance for your answers.



  • AdelaideRAdelaideR Member admin

    Hi @lindenb

    I believe that it may be useful for you to upgrade to the latest version of GATK which has reduced the time and compute costs of running these analyses.

    Many of these improvements are described in our release notes.

    I think that will resolve these issues.

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