Issues

• Get guacamole and friends building on newest batch of shared libraries

  infrastructure
  hammerlab/guacamole#616 · Filter by author hammer opened on Dec 17, 2016
  1

  

• Make indel realignment splice aware

  hammerlab/guacamole#615 · Filter by author hammer opened on Dec 8, 2016
  1

• --loci argument conflicts with TakeLociIterator

  hammerlab/guacamole#611 · Filter by author arahuja opened on Oct 26, 2016
  2

• throwed exception: ./scripts/guacamole: line 39 :exec: time: not found

  hammerlab/guacamole#572 · Filter by author car2008 opened on Sep 9, 2016
  27

• Move to Spark 2.0

  hammerlab/guacamole#566 · Filter by author arahuja opened on Sep 1, 2016
  2

• Send relevant reference sequences to executors in more fine-grained ways than via a Broadcast

  infrastructure
  hammerlab/guacamole#560 · Filter by author ryan-williams opened on Aug 20, 2016

• Allow receiving inputs from config files

  infrastructure
  hammerlab/guacamole#553 · Filter by author ryan-williams opened on Aug 15, 2016
  

• Remove progress helper, use Spark/log4j

  enhancementinfrastructure
  hammerlab/guacamole#551 · Filter by author ryan-williams opened on Aug 15, 2016
  

• Test running on Baylor "case 2" dataset

  validation
  hammerlab/guacamole#548 · Filter by author ryan-williams opened on Aug 15, 2016
  2

  

• Allow reference file to be loaded from HDFS or GS

  infrastructure
  hammerlab/guacamole#512 · Filter by author arahuja opened on Jul 28, 2016
  

• Is there any way we can get the quali and filter information in the vcf file.

  hammerlab/guacamole#470 · Filter by author ankushreddy opened on May 2, 2016

• consider supporting other output formats (csv, json, arrow?) in joint caller

  infrastructure
  hammerlab/guacamole#447 · Filter by author timodonnell opened on Apr 22, 2016
  2

• Ensure VCFs comply with the VCFv4.1 spec

  infrastructure
  hammerlab/guacamole#442 · Filter by author e5c opened on Apr 13, 2016

• Codify style rules

  infrastructure
  hammerlab/guacamole#439 · Filter by author ryan-williams opened on Apr 12, 2016
  7

• Upgrade to Scala 2.11

  infrastructure
  hammerlab/guacamole#438 · Filter by author ryan-williams opened on Apr 12, 2016
  5

• support writing Guacamole commands in separate projects

  infrastructure
  hammerlab/guacamole#424 · Filter by author timodonnell opened on Apr 4, 2016
  2

• Allow for reading in block gzip compressed VCF files.

  infrastructure
  hammerlab/guacamole#402 · Filter by author jstjohn opened on Mar 26, 2016
  2

• joint caller: use phasing information for better calls

  variant calling
  hammerlab/guacamole#390 · Filter by author timodonnell opened on Feb 29, 2016

• joint caller: output phasing information

  variant calling
  hammerlab/guacamole#389 · Filter by author timodonnell opened on Feb 29, 2016
  1

  

• Potential source of validated somatic mutations

  validation
  hammerlab/guacamole#387 · Filter by author hammer opened on Feb 25, 2016
  2

• joint caller: implement filters

  variant calling
  hammerlab/guacamole#385 · Filter by author timodonnell opened on Feb 16, 2016
  3

  

• Null alleles error.

  hammerlab/guacamole#379 · Filter by author ankushreddy opened on Feb 3, 2016
  4

• when ever am passing a bam file as input am getting nothing out of this.

  hammerlab/guacamole#375 · Filter by author ankushreddy opened on Jan 27, 2016
  12

• Some more light on how to use the reference files.

  hammerlab/guacamole#374 · Filter by author ankushreddy opened on Jan 26, 2016
  1

• Ensure test BAM files are valid

  validation
  hammerlab/guacamole#370 · Filter by author hammer opened on Jan 8, 2016
  2