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Realignment using assembly to pick variants #200

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fnothaft opened this issue Jan 17, 2017 · 0 comments
Open

Realignment using assembly to pick variants #200

fnothaft opened this issue Jan 17, 2017 · 0 comments
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We should use the assembly code to pick out INDEL variants that are then thrown into the ADAM indel realigner's "known INDELs" mode.
@fnothaft fnothaft self-assigned this Jan 17, 2017
@fnothaft fnothaft added this to the 0.1.0 milestone Jan 17, 2017
@fnothaft fnothaft mentioned this issue Jan 18, 2017
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fnothaft added a commit to fnothaft/avocado that referenced this issue Jan 23, 2017
@fnothaft
[AVOCADO-200] Feed assembled variants to INDEL realigner.
9c7094c 
Resolves bigdatagenomics#200. Depends on bigdatagenomics/adam#1363.

* Adds a ConsensusRealigner that uses the main Realigner to realign reads,
  which are then fed into the variant discovery engine with loose filters. Any
  INDEL variants that are discovered are then fed in to ADAM's INDEL realignment
  engine as known INDELs.
* Uses this realignment mode in the BiallelicGenotyperSuite to clean up a
  previously failing test.
* Adds this to the Reassemble CLI as a `-use_consensus_realigner` switch.
fnothaft added a commit to fnothaft/avocado that referenced this issue Jan 25, 2017
@fnothaft
[AVOCADO-200] Feed assembled variants to INDEL realigner.
908349d 
Resolves bigdatagenomics#200. Depends on bigdatagenomics/adam#1363.

* Adds a ConsensusRealigner that uses the main Realigner to realign reads,
  which are then fed into the variant discovery engine with loose filters. Any
  INDEL variants that are discovered are then fed in to ADAM's INDEL realignment
  engine as known INDELs.
* Uses this realignment mode in the BiallelicGenotyperSuite to clean up a
  previously failing test.
* Adds this to the Reassemble CLI as a `-use_consensus_realigner` switch.
fnothaft added a commit to fnothaft/avocado that referenced this issue Feb 28, 2017
@fnothaft
[AVOCADO-200] Feed assembled variants to INDEL realigner.
57a7e64 
Resolves bigdatagenomics#200. Depends on bigdatagenomics/adam#1363.

* Adds a ConsensusRealigner that uses the main Realigner to realign reads,
  which are then fed into the variant discovery engine with loose filters. Any
  INDEL variants that are discovered are then fed in to ADAM's INDEL realignment
  engine as known INDELs.
* Uses this realignment mode in the BiallelicGenotyperSuite to clean up a
  previously failing test.
* Adds this to the Reassemble CLI as a `-use_consensus_realigner` switch.
@fnothaft fnothaft mentioned this issue Feb 28, 2017
Open
fnothaft added a commit to fnothaft/avocado that referenced this issue Mar 1, 2017
@fnothaft
[AVOCADO-200] Feed assembled variants to INDEL realigner.
e96ddea 
Resolves bigdatagenomics#200. Depends on bigdatagenomics/adam#1363.

* Adds a ConsensusRealigner that uses the main Realigner to realign reads,
  which are then fed into the variant discovery engine with loose filters. Any
  INDEL variants that are discovered are then fed in to ADAM's INDEL realignment
  engine as known INDELs.
* Uses this realignment mode in the BiallelicGenotyperSuite to clean up a
  previously failing test.
* Adds this to the Reassemble CLI as a `-use_consensus_realigner` switch.
@fnothaft fnothaft removed this from the 0.1.0 milestone Jan 5, 2018
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