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run CombineGVCFs per chromosome and merge with CatVariants?

KinMokKinMok LondonMember

I try to combine 56 low coverage exomes gvcf produced by Haplotypecaller GVCF mode. It take 5+ days if I perform the combination of 56gvcf all in one go. I try CombineGVCFs on per chr basis using -L with command as

java $JAVAmem -jar $GATKPATH/GenomeAnalysisTK.jar -T CombineGVCFs \
-R "$REFfasta" \
-L 1 \
--variant $IN/001.AllChr.raw.snps.indels.gvcf \
to
--variant $IN/056.AllChr.raw.snps.indels.gvcf \
-o $OUT/mergeChr1.raw.snps.indels.gvcf

After getting the combined files per chromosome, am I right that I should use CatVariants to combine them to a mega file rather than using CombineGVCFs again ?

Thanks

Kin

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