-
I wonder what is the error model difference between WGS and WES. Is it simply the way coverage varies, or is there any difference in the error rates/types?
Also for the open training [data](https:/…
-
## Feature request
### Tool(s) involved
MarkDuplicates
### Description
If an input bam/cram is provided to MarkDuplicates that does not contain a `@RG` header line, then MarkDuplicates should …
-
@ewels built https://github.com/ewels/AWS-iGenomes and we should provide a list of files that are going to be sent to S3 so one can set up CAW references files easily.
-
the goal is to be at least same as gatk3.4 on single thread. This is for the walker version of the tools.
The ticket can be split into a) profile and b) optimize if needed
-
`VariantFiltration` in GATK4 with clustered SNP filtering on is likely to underperform GATK3, as this results in queries against the driving source of variants both before and after the current varian…
-
After https://github.com/broadinstitute/gatk/pull/792 is merged, ensure that our version of `SelectVariants` is as fast or faster than the GATK3 version on typical inputs.
-
the goal is to be at least same as gatk3.4 on single thread. This is for the walker version of the tool.
The ticket can be split into a) profile and b) optimize if needed
Note: the GATK3.4 version is…