guacamole
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hammerlab
Spark-based variant calling, with experimental support for multi-sample somatic calling (including RNA) and local assembly
Porting this from @ryan-williams's 12/12 status report so that we can start tracking our work accurately on GitHub!
@jstjohn [discussed hitting some issues](https://github.com/hammerlab/guacamole/issues/386#issuecomment-198755271) running on the "case 2" data [here](http://txcrb.org/data.html#registration). I'm downloading the data now to attempt to reproduce.
The assumption for things like `SomaticStandardCaller` (or others that use `pileupFlatMap`) is that `--loci` controls the loci at which to examine pileups. However, when using `CappedRegionsPartitioner` this is not the...
Hi , my command is `./scripts/guacamole somatic-joint /home/zhipeng/soft/guacamole/src/test/resources/synth1.normal.100k-200k.withmd.bam /home/zhipeng/soft/guacamole/src/test/resources/synth1.tumor.100k-200k.withmd.bam --reference-fasta /home/zhipengcheng/file/ucsc.hg19.fasta --out /home/zhipengcheng/file/result/out.vcf` but it throwed exception : > ./scripts/guacamole: line 39 :exec: time: not found I don't know how...
Eventually we should do this; collecting notes about how/when here. - should we have a transition period where we support both? - or should we switch over in one go...
I recently removed Scalariform due to conflicts between it, my personal preferences, and (most importantly) IntelliJ that I wasn't able to resolve. In #435, #436, and #437, some questions have...
It seems like this will involve: - removing/moving references `org.apache.spark.logging` - upgrading ADAM - upgrading `spark-testing-base` to `2.0.0_0.4.4` @ryan-williams have you tried this out already, I remember you were looking...
Possible contenders: 1) Scalameter http://scalameter.github.io/ Used by: http://scala-miniboxing.org/, but not sure how to connect to maven/build process 2) Google Caliper https://code.google.com/p/caliper/ Java, used by: https://github.com/scalanlp/breeze