anr
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Latest activity by anr-
anr commented,
Hi Genevieve Brandt (she/her): I'm running the GATK joint genotyping WARP pipeline, using GATK predefined interval list on 174 human samples. While I get multiple regions with multiple genotypes I ...
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anr commented,
Gökalp Çelik: This issue seems to be cromwell on GCP. "message": "Failed to evaluate 'files_in_partition' (reason 1 of 1): Evaluating read_lines(PartitionSampleNameMap.partitions[idx]) failed: Fail...
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anr commented,
Hi, I'm trying to implement GATK's WARP joint genotyping pipeline on google cloud platform. I'm getting all sorts of Cromwell errors with read_tsv and read_lines functions. What is the workaround f...
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anr commented,
Hi Nalini Ganapati: Thank you for the response. Yes I have been read the performance guidelines blog. By local genomicsdb do you mean to have a copy of the genomicsdb in the VM the job is running i...
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anr created a post,
GenomicsDBImport for joint genotyping
AnsweredHi Nalini Ganapati: Im reposting here per your request about my question on GenomicsDBI import. We have 238 wgs samples sequenced at 30X coverage, I've used GenotypeGVCFs on 3 samples for joint-gen...
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anr commented,
Lucas Taniguti Nalini Ganapati : I'm trying to use GenomicsDBImport on 238 wgs samples sequenced to 30X on all intervals on google cloud. Is there anything that I should keep in mind when implement...