jfarrell
- Total activity 14
- Last activity
- Member since
- Following 0 users
- Followed by 0 users
- Votes 0
- Subscriptions 5
Comments
Recent activity by jfarrell Sort by recent activity-
This link below is broken from above. Has there been an update with the Tutorial which matches the latest WDL pipeline? ftp://ftp.broadinstitute.org/tutorials/dataset Download tutorial_11684.ta...
-
kvn95ss and Genevieve Brandt (she/her) Regarding the bypass-feature reader recommendation, the documentation mentions the VCFs must be normalized. Are reblocked gvcfs normalized and ready to use o...
-
To use the --bypass-feature-reader option for GenomicsDBImport, the documentation indicates the VCF must be normalized, block compressed and indexed. Use htslib to read input VCFs instead of GA...
-
This is a potential solution that I will be testing out with my next batch of crams. There is now support in the 4.2.6.1 CombineGVCFs and GenotypeGVCFs for "reblocked" GVCFs as produced by the Rebl...
-
It runs to completion if I give the job a lot of memory (80 -120 gb) and target a small interval for the genomicsDB with 2000 samples for each chromosome. The output vcf.gz is only 55M for onl...
-
These are useful suggestions on speeding up GenotypwGVCFs which I am using. None of them address the large amount of memory used no matter how small the target size that is specified. GenotypeGVC...
-
Based on some runs with GATK 4.2.0.0, it does seem to use a lot of memory no matter the size of the interval and it correlates with the size of the chromosome. The memory used increases as the c...
-
Where is the documentation for the ComposeSTRTableFile tool referenced in this article? Don't see it in the Tools Documentation.