Tim O'Donnell

Looks like your shell doesn't have the "time" command. Try just deleting the word "time" from the last line of scripts/guacamole, i.e. instead of: exec time java -Xmx4g -XX:MaxPermSize=512m "-Dspark.master=local[1]"...

One of the most important filters to have: filter somatic calls that have evidence in the normal (i.e. cases where the variant is present in the normal at too low...

Mutect filters / annotations we need (much of this is based on [here](https://www.broadinstitute.org/gatk/events/slides/1506/GATKwr8-S-3-Variant_calling_with_MuTect.pdf)) - [X] Evidence in normal - [X] Strand bias - [X] triallelic site - [ ] proximal...

What does "tasks are now broadcast anyways" mean? On Tue, Nov 25, 2014 at 9:28 AM, Arun Ahuja [email protected] wrote: > Most job on a full genome print the following...

Bumping this. I'd like to be able to directly load a VCF generated by guacamole into varcode, and be able to run guacamole repeatedly and have it just overwrite the...

Thanks for the contribution @jstjohn . Looks awesome. Couple of quick comments (we'll add more as people look at this in more depth): - I think it'd be helpful to...

If you think this is a good idea, Arun, I'm not opposed On Thu, Jul 16, 2015 at 4:41 PM, Arun Ahuja [email protected] wrote: > OK, I have no strong...

@arahuja I somehow missed your comment before, sorry about that. I think having an example of such a command is a good idea. Maybe we could add a directory to...

Yeah @hammer suggests json

One file we need to fix is: https://github.com/hammerlab/guacamole/blob/continue-somatic-joint/src/test/resources/illumina-platinum-na12878-extract/NA12878.10k_variants.plus_chr1_3M-3.1M.chr_fixed.bam When running from that branch (continue-somatic-joint), we're getting: ``` (analysis-venv-2.7)[tim@Tims-MacBook ~/sinai/git/guacamole]$ scripts/guacamole somatic-joint /Users/tim/sinai/git/guacamole/target/scala-2.10.3/test-classes/illumina-platinum-na12878-extract/NA12878.10k_variants.plus_chr1_3M-3.1M.chr_fixed.bam --reference-fasta /Users/tim/sinai/data/ucsc.hg19.fasta.gz --loci chr1:0-6700000 Using most recently modified...