Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[ADAM-1362] Fixing issue where FromKnowns consensus model fails if no reads hit a target. #1363

Merged

Conversation

@fnothaft
Copy link
Member

fnothaft commented Jan 23, 2017

Fixes #1362:

  • Adding ConsensusGeneratorFromKnownsSuite.
  • ConsensusGeneratorFromKnowns drops any targets that did not get hit with any reads, instead of trying to identify the full reference region overlapped by reads. While this case (target with no reads) cannot happen in the FromReads consensus model, it can happen in the FromKnowns model (e.g., use all known INDELs from 1000G with a WES dataset).
  • Additionally, tracked down a minor off by one bug in RealignIndels that caused one index in the consensus sequence to not get tested. This could cause reads that aligned to the end of the target to not get realigned.
  • To improve legibility, broke up a set of long lines in RealignIndels.
… reads hit a target.

Fixes #1362:

* Adding ConsensusGeneratorFromKnownsSuite.
* ConsensusGeneratorFromKnowns drops any targets that did not get hit with any
  reads, instead of trying to identify the full reference region overlapped by
  reads. While this case (target with no reads) cannot happen in the FromReads
  consensus model, it can happen in the FromKnowns model (e.g., use all known
  INDELs from 1000G with a WES dataset).
* Additionally, tracked down a minor off by one bug in RealignIndels that caused
  one index in the consensus sequence to not get tested. This could cause reads
  that aligned to the end of the target to not get realigned.
* To improve legibility, broke up a set of long lines in RealignIndels.
@fnothaft fnothaft added this to the 0.21.1 milestone Jan 23, 2017
@fnothaft fnothaft requested a review from heuermh Jan 23, 2017
@AmplabJenkins
Copy link

AmplabJenkins commented Jan 23, 2017

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1748/
Test PASSed.

fnothaft added a commit to fnothaft/avocado that referenced this pull request Jan 23, 2017
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.
@heuermh heuermh merged commit 00dc230 into bigdatagenomics:master Jan 23, 2017
1 check passed
1 check passed
default Merged build finished.
Details
@heuermh
Copy link
Member

heuermh commented Jan 23, 2017

Thank you, @fnothaft!

fnothaft added a commit to fnothaft/avocado that referenced this pull request Jan 25, 2017
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 pull request Feb 28, 2017
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 pull request Mar 1, 2017
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.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Linked issues

Successfully merging this pull request may close these issues.

None yet

3 participants
You can’t perform that action at this time.