Intersect exome region from whole genome gvcf

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4.4 years ago

MAPK ★ 2.1k

I have been trying to get a joint genotype for exome bed region from whole genome gvcf. However, this is really slow and I am not sure if this is the right approach to do it. I have more than 600 samples and this has been running for more than 10 days. Can someone please clarify?

module load java
/gatk-4.1.7.0/gatk --java-options "-Xms4G -Xmx32G -DGATK_STACKTRACE_ON_USER_EXCEPTION=true" \
 GenomicsDBImport \
--genomicsdb-workspace-path /scratch/chr19 \
--batch-size 50 \
-L /scratch/chr19.exome.bed \
--sample-name-map /scratch/AllSamplesGvcfChr19.list \
--reader-threads 16

gatk GenomicsDBImport • 1.1k views

ADD COMMENT • link 4.4 years ago by MAPK ★ 2.1k

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I got the same problem, at the end I moved back to gatk/CombineGVCF ...

ADD REPLY • link 4.4 years ago by Pierre Lindenbaum 164k

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Was it faster? Did you do GenotypeGVCFs afterwards?

ADD REPLY • link 4.4 years ago by MAPK ★ 2.1k

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yes and yes

ADD REPLY • link 4.4 years ago by Pierre Lindenbaum 164k

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