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