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3. GATK Liftover memory issues on cohort vcf

Yes, thank you that ended up working; it just required a ton of memory. 

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• Jose Arcadio Buendia
• September 02, 2020 14:12
• 0 votes

1. Community
2. Germline
3. GATK Liftover memory issues on cohort vcf

gatk LiftoverVcf --TMP_DIR tmp/ -I test.vcf -O out.vcf --CHAIN /igm/home/liftover/Hg38Tob37.over.chain --REJECT out.rejected.vcf -R /igm/apps/genomes/Homo_sapiens/human_g1k_v37_decoy/human_g1k_v37_...

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• Jose Arcadio Buendia
• August 25, 2020 14:28
• 0 votes

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2. Other
3. Out of memory error using OpenJDK vs Oracle JDK for CNV-LOH

Switching to OpenJDK Hotspot solved the issue! Thanks you!

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• Jose Arcadio Buendia
• March 03, 2020 22:43
• 1 vote