GitHub PushEvent at 2014-08-22 19:07:23
Repository: Exome-vc-pipelineV2
Actor: AshKernow
Payload: {"shas":[["19881dbb0f4eaa4cb72e3971f00ca9f076883332","efeea00b2e4319ab34d9da6de656bd04af5efe10@c2b2.columbia.edu","Added BadET option","Ashley Sawle",true],["5685252eb3bea80c1c0a8361cc31516cdff857fc","efeea00b2e4319ab34d9da6de656bd04af5efe10@c2b2.columbia.edu","Added FixMisencoded option. Changed the filename from the SampleID to the original bam file name. Replaced htscmd with samtools.","Ashley Sawle",true],["855c5d92ffaddbfeb388417f70e7310848fad3ff","efeea00b2e4319ab34d9da6de656bd04af5efe10@c2b2.columbia.edu","Replaced htscmd with samtools.","Ashley Sawle",true],["8e3f452f9d3ea5d1ee73e36a919f2415f2a9b79c","efeea00b2e4319ab34d9da6de656bd04af5efe10@c2b2.columbia.edu","Increase time allocation.","Ashley Sawle",true],["11991907f7909af8c0e038f7a37ef2a7d0ea502f","efeea00b2e4319ab34d9da6de656bd04af5efe10@c2b2.columbia.edu","Increase time allocation. Add function to accept list. Switch to call new ExmAln.5.BaseQualityScoreRecalibration.sh script.","Ashley Sawle",true],["6b6c51876b4a9fdf6f93e44f81b2729d7a757735","efeea00b2e4319ab34d9da6de656bd04af5efe10@c2b2.columbia.edu","New unified BQSR script. Pipeline straight into gvcf creation. Remove pipeline into depth of coverage","Ashley Sawle",true],["0b05e01f76244e1389b9554220e9cf1e7bf855fc","efeea00b2e4319ab34d9da6de656bd04af5efe10@c2b2.columbia.edu","Altered to keep full DoC details file.","Ashley Sawle",true],["73c05f03ee4f84054dfe40170ea7517eca81d3f6","efeea00b2e4319ab34d9da6de656bd04af5efe10@c2b2.columbia.edu","Move gvcf creation to end of alignment pipeline","Ashley Sawle",true],["dc7311466d0f15abd08ee8c3dc72fc64d58445f4","efeea00b2e4319ab34d9da6de656bd04af5efe10@c2b2.columbia.edu","Change to pipeline names","Ashley Sawle",true],["41242c22888c452d0c9e02234d305f9eedee1f3b","efeea00b2e4319ab34d9da6de656bd04af5efe10@c2b2.columbia.edu","Removed info annotation from annotation call - was causing a crash.","Ashley Sawle",true],["e0878c1a73773ba497ab2140a5fadf30fd6d6f66","efeea00b2e4319ab34d9da6de656bd04af5efe10@c2b2.columbia.edu","Change of name as merge now used with both UG and HC","Ashley Sawle",true],["f68c461a7b1cd5f7fb0dbe6509f0d88f6f423414","efeea00b2e4319ab34d9da6de656bd04af5efe10@c2b2.columbia.edu","New ad hocs and filters. Functional.","Ashley Sawle",true],["e5fa73ac06cc1a1bd9fa0c54caaf47f47037c562","efeea00b2e4319ab34d9da6de656bd04af5efe10@c2b2.columbia.edu","Reference file using Yufengs hg19 reference","Ashley Sawle",true],["df914330ade64f4df85e2a7b8877880c4eb00377","efeea00b2e4319ab34d9da6de656bd04af5efe10@c2b2.columbia.edu","Rewrite to bring variable names in line with other scripts","Ashley Sawle",true],["47ae145cd485bf86ab28dab7b395f3d22d4a8009","efeea00b2e4319ab34d9da6de656bd04af5efe10@c2b2.columbia.edu","Minor reporting change","Ashley Sawle",true],["f3c7f68bf7c32ffc42317c1fce3eb295ca12feb3","efeea00b2e4319ab34d9da6de656bd04af5efe10@c2b2.columbia.edu","Changes to file locations","Ashley Sawle",true],["f5438317207a7df184335e90ad5a2f74ae87848d","efeea00b2e4319ab34d9da6de656bd04af5efe10@c2b2.columbia.edu","Added reference file to log output. Added extra line to gatk log trimming","Ashley Sawle",true],["a92dbdfb887a62db9d6dae9dbf38e14eda95073d","efeea00b2e4319ab34d9da6de656bd04af5efe10@c2b2.columbia.edu","Changes to cope with mutliple annotations","Ashley Sawle",true],["a6bd7b33a32949564e5e595d5d615ed935764f49","efeea00b2e4319ab34d9da6de656bd04af5efe10@c2b2.columbia.edu","New HC joint calling script allowing scatter-gather parallelization.","Ashley Sawle",true]],"size":19,"ref":"refs/heads/master","head":"a6bd7b33a32949564e5e595d5d615ed935764f49"}