Nalini Ganapati
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Latest activity by Nalini Ganapati-
Nalini Ganapati commented,
You will have to list the superset of scaffold contigs you are expecting as -L options. Unfortunately, in your case, that could run into tens of thousands, so you may have to resort to creating an ...
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Nalini Ganapati commented,
Please try the --merge-contigs-into-num-partitions option with gatk GenomicsDBImport. --merge-contigs-into-num-partitions <Integer> Number of GenomicsDB arrays to merge input intervals into....
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Nalini Ganapati commented,
@anr, that custom library was only for testing purposes and may not work now. Please use the latest gatk available. Actually, I meant use a genomicsdb workspace on your local filesystem. Something ...
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Nalini Ganapati commented,
@anr, there are no particular optimal memory settings to use with GenomicsDBImport and SelectVariants as far as GVCFs on the cloud are concerned. I'd suggest you use a local genomicsdb workspace wi...
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Nalini Ganapati commented,
Another thing, you may also need to invoke GenotypeGVFs with the --genomicsdb-shared-posixfs-optimizations if your workspace is on NFS/Lustre.
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Nalini Ganapati commented,
For 1000 WGS, partitioning by chromosome might be very resource intensive for both import and querying and you may have to partition your intervals with lesser granularity(e.g chr22:1-10000) if pos...
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Nalini Ganapati commented,
Using GenomicsDBImport on the test vcf provided threw the following exception %: ./gatk --java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true' GenomicsDBImport -L 1:883600-883650 -V ex001.mutec...
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Nalini Ganapati commented,
Hi Bernt, From the gatk docs for GenomicsDBImport, --reader-threads is for reading vcfs only. For the import itself, you will have to use the --max-num-intervals-to-import-in-parallel option. Of co...