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Work on getting Mutect algorithm up and running #167

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Work on getting Mutect algorithm up and running #167

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Commits on Apr 25, 2015

  1. Added base quality score based read filters.

    @tdanford @fnothaft
    tdanford authored and fnothaft committed Apr 25, 2015
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  2. Miscellaneous read filter cleanup. Refactored preprocessing stages th… 

    …at filter reads to have a consistent interface.

Using this interface, I added filters to eliminate reads with high levels of soft clipping, and reads that are marked as duplicates.
    @fnothaft
    fnothaft committed Apr 25, 2015
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  3. Updates to depth filter. Genotypes are not discarded, rather the filt… 

    …er string is set.

Further, refactored depth filter to provide generalized attribute based genotype filter.
Using generalized filter, added strand bias filter and multiallelic site filter.
    @fnothaft
    fnothaft committed Apr 25, 2015
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Commits on May 13, 2015

  1. adding in @tdanford's mutect work, merging into current avocado

    @jstjohn
    jstjohn committed May 13, 2015
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  2. Merge branch 'master' into jsj_mutect_hack

    @jstjohn
    jstjohn committed May 13, 2015
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Commits on May 14, 2015

  1. Merge branch 'common-filters' of github.com:fnothaft/avocado into jsj… 

    …_mutect_fnothaft
    @jstjohn
    jstjohn committed May 14, 2015
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  2. Merge branch 'master' of github.com:bigdatagenomics/avocado into jsj_… 

    …mutect_fnothaft
    @jstjohn
    jstjohn committed May 14, 2015
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Commits on May 17, 2015

  1. restoring successful compile with in-progress mutect against lastest … 

    …version of adam/avocado
    @jstjohn
    jstjohn committed May 17, 2015
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  2. Merge branch 'common-filters' of github.com:fnothaft/avocado into mut… 

    …ect_work
    @jstjohn
    jstjohn committed May 17, 2015
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Commits on May 18, 2015

  1. pulling over MuTect LikelihoodModel, fixing some bugs, and making tests

    @jstjohn
    jstjohn committed May 18, 2015
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  2. initial pull over of Mutect.scala base function, and a base suite of … 

    …tests which will be filled in
    @jstjohn
    jstjohn committed May 18, 2015
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  3. more fixes and clarifications on the mutect likelihood model

    @jstjohn
    jstjohn committed May 18, 2015
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  4. adding in initial tests of likelihood given an actual mutation

    @jstjohn
    jstjohn committed May 18, 2015
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  5. added in tests for mutant site

    @jstjohn
    jstjohn committed May 18, 2015
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  6. reorganizing tests slightly

    @jstjohn
    jstjohn committed May 18, 2015
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  7. added in a final test covering the normal somatic classification

    @jstjohn
    jstjohn committed May 18, 2015
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  8. Adding mutect tests and TODO comments to main code

    @jstjohn
    jstjohn committed May 18, 2015
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Commits on May 19, 2015

  1. adding somatic classification code/tests into MuTect

    @jstjohn
    jstjohn committed May 19, 2015
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  2. making test reads slightly more realistic, assigned to both strands now

    @jstjohn
    jstjohn committed May 19, 2015
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  3. adding a small mutect test for sites with no tumor coverage, but some… 

    … normal reads
    @jstjohn
    jstjohn committed May 19, 2015
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Commits on May 20, 2015

  1. Merge branch 'master' into mutect_work

    @jstjohn
    jstjohn committed May 20, 2015
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Commits on May 26, 2015

  1. cleaning up code, refactoring location of Mutect.scala, adding in lic… 

    …enses
    @jstjohn
    jstjohn committed May 26, 2015
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  2. Adding harness for running Mutect algorithm on real reads.

    @fnothaft
    fnothaft committed May 26, 2015
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  3. switching to phredToErrorProbability from internal function

    @jstjohn
    jstjohn committed May 26, 2015
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  4. Merge pull request #1 from fnothaft/mutect-runner 

    Adding harness for running Mutect algorithm on real reads.
    @jstjohn
    jstjohn committed May 26, 2015
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  5. adding license header to MutectGenotyperSuite and removing old versions

    @jstjohn
    jstjohn committed May 26, 2015
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Commits on May 27, 2015

  1. merging in new AlleleObservation code from Master, updating tests

    @jstjohn
    jstjohn committed May 27, 2015
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Commits on May 30, 2015

  1. Adding more pre-processing filters for Mutect.

    @tdanford @fnothaft
    tdanford authored and fnothaft committed May 30, 2015
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  2. Merge pull request #2 from fnothaft/mo-mutect 

    Adding more pre-processing filters for Mutect.
    @jstjohn
    jstjohn committed May 30, 2015
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  3. adding 5 fields to AlleleObservation for allele-specific filtering: d… 

    …istanceToNearestReadInsertion, distanceToNearestReadDeletion, clippedBasesReadStart, clippedBasesReadEnd, unclippedReadLen
    @jstjohn
    jstjohn committed May 30, 2015
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  4. Adding two new fields to AlleleAlleleObservation to store the distanc… 

    …e from this allele to the left, and right soft/hard trimmed base, if it exists
    @jstjohn
    jstjohn committed May 30, 2015
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  5. soft clipped read should have the clipped bases in the sequence

    @jstjohn
    jstjohn committed May 30, 2015
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Commits on May 31, 2015

  1. initial calculation of distance from each allele to nearest indel and… 

    … soft clipped base within each read
    @jstjohn
    jstjohn committed May 31, 2015
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Commits on Jun 1, 2015

  1. Tests pass ReadExplorer, adding initial version using those filters t… 

    …o MutectGenotyper
    @jstjohn
    jstjohn committed Jun 1, 2015
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Commits on Jun 2, 2015

  1. implementing more mutect filters, and adding TODOs for the last few f… 

    …ilters MuTect needs internally
    @jstjohn
    jstjohn committed Jun 2, 2015
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  2. putting magic numbers into config variables

    @jstjohn
    jstjohn committed Jun 2, 2015
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  3. implement the allele cluster filter

    @jstjohn
    jstjohn committed Jun 2, 2015
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  4. removing unneeded fields from AlleleObservation and replacing with a … 

    …cleaner way to get the information I need in MuTect
    @jstjohn
    jstjohn committed Jun 2, 2015
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  5. adding more tests to Mutect internal filters

    @jstjohn
    jstjohn committed Jun 2, 2015
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  6. passing mate rescue status through to AlleleObservation

    @jstjohn
    jstjohn committed Jun 2, 2015
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  7. adding in custom mutect strand bias method

    @jstjohn
    jstjohn committed Jun 2, 2015
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  8. fixing bug in MutectGenotyper tests where filters were not being prop… 

    …erly tested, and fixed bug in filters so they work now
    @jstjohn
    jstjohn committed Jun 2, 2015
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Commits on Jun 3, 2015

  1. refactoring variables to camelCase

    @jstjohn
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  2. faster O(log(n)) recursive search for minimal passing k value

    @jstjohn
    jstjohn committed Jun 3, 2015
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Commits on Jun 4, 2015

  1. cleaning up code a bit

    @jstjohn
    jstjohn committed Jun 4, 2015
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  2. cleaning up variable names

    @jstjohn
    jstjohn committed Jun 4, 2015
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Commits on Jun 10, 2015

  1. Implementation of the sum of mismatching quality scores in the Allele… 

    …Observation object and parsed from read MD tags by ReadExplorer
    @jstjohn
    jstjohn committed Jun 10, 2015
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Commits on Jun 26, 2015

  1. Merge branch 'master' of github.com:bigdatagenomics/avocado into mute… 

    …ct_work
    @jstjohn
    jstjohn committed Jun 26, 2015
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Commits on Jul 1, 2015

  1. Merge branch 'master' of github.com:bigdatagenomics/avocado into mute… 

    …ct_work
    @jstjohn
    jstjohn committed Jul 1, 2015
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Commits on Aug 1, 2015

  1. Adding known-sites variant filter.

    @fnothaft
    fnothaft committed Aug 1, 2015
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  2. Merge pull request #3 from fnothaft/add-dbsnp 

    Adding known-sites variant filter.
    @jstjohn
    jstjohn committed Aug 1, 2015
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Commits on Aug 3, 2015

  1. Added site detection to mutect genotyper. Also, made site filter and … 

    …genotyper use broadcast.
    @fnothaft
    fnothaft committed Aug 3, 2015
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  2. Fixed MD tag bug caused by upstream change to MD tag code in ADAM.

    @fnothaft
    fnothaft committed Aug 3, 2015
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  3. Merge pull request #4 from fnothaft/add-dbsnp 

    Add dbsnp to mutect caller
    @jstjohn
    jstjohn committed Aug 3, 2015
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Commits on Aug 30, 2015

  1. adding in the required settings to enable Panel of Normal (PON) filte… 

    …ring as discussed in the MuTect paper
    @jstjohn
    jstjohn committed Aug 30, 2015
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  2. Merge branch 'master' of github.com:bigdatagenomics/avocado into mute… 

    …ct_work
    @jstjohn
    jstjohn committed Aug 30, 2015
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Commits on Jan 7, 2016

  1. Merge pull request #2 from bigdatagenomics/master 

    Updating from bigdatagenomics/avocado
    @stewSquared
    stewSquared committed Jan 7, 2016
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  2. Merge branch 'master' into mutect_work

    @stewSquared
    stewSquared committed Jan 7, 2016
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Commits on Jan 8, 2016

  1. Merge pull request #3 from bigdatagenomics/master 

    Update ADAM to 0.18.2
    @stewSquared
    stewSquared committed Jan 8, 2016
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  2. Merge branch 'master' into mutect_work

    @stewSquared
    stewSquared committed Jan 8, 2016
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Commits on Jan 28, 2016

  1. Added support for having 2 input ADAM reads file, with the option to … 

    …label reads. Runs with MuTect, but there are bugs within the program
    Isabel Chien authored and Isabel Chien committed Jan 28, 2016
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Commits on Mar 10, 2016

  1. implementing isabels changes

    @jstjohn
    jstjohn committed Mar 10, 2016
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Commits on Mar 11, 2016

  1. adding isabels changes

    @jstjohn
    jstjohn committed Mar 11, 2016
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