e185632013Exhaustive unit tests for Pool SNP genotype likelihoods: a) Add ability for ErrorModel to be specified by external log-probability vector for testing. b) For a given depth and ploidy(=2*samples/pool), create artificial high quality pileup testing from AC=0 to AC=ploidy, and test that pool GL's have expected content.Misc. refactorings and cleanups c) Misc. cleanups and beautification.
Guillermo del Angel
2012-04-30 14:29:46 -0400
7d029b9a28Merge branch 'master' of ssh://ni.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Christopher Hartl
2012-04-30 12:16:30 -0400
944a7d815eBringing VQSRV3 up to date. Lots of new features (un-classifying the worst-performing training sites, treating the x% best/worst sites as postive/negative points, ability to pass in a monomorphic track to see ROC curves output). Minor changes to AlleleBalance: weighted average was incorrectly specified (using logscale actually biased the average towards the AB of low-quality genotypes), and breaking out AB by het, hom, and diploid to bring it in line with some (private) changes to the indel likelihood model that (correctly) computes these values for indels.
Christopher Hartl
2012-04-28 11:31:03 -0400
54a9bc2da2Bug fix in reverse trim alleles for the case of mixed records that become non-mixed after subsetting the alleles.
Ryan Poplin
2012-04-28 09:12:26 -0400
e332aeaf70Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-04-27 16:21:21 -0400
2b5dd28550Bug fix in reverse trim alleles for the case of mixed records.
Ryan Poplin
2012-04-27 16:21:02 -0400
1db2d1ba82Do not add the first and last 4 cycles to the recalibration tables.
Mauricio Carneiro
2012-04-26 13:32:38 -0400
08dbd756f3Quick QC walkers to look at the error profile of indels in the read
Mauricio Carneiro
2012-04-25 17:09:36 -0400
24173d860aMerge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Guillermo del Angel
2012-04-27 14:41:38 -0400
730208133bSeveral fixes and improvements to Pool caller with ancillary test functions (not done yet): a) Utility class called Probability Vector that holds a log-probability vector and has the ability to clip ends that deviate largely from max value. b) Used this class to hold site error model, since likelihoods of error model away from peak are so far down that it's not worth computing with them and just wastes time. c) Expand unit tests and add an exhaustive test for ErrorModel class. d) Corrected major math bug in ErrorModel uncovered by exhaustive test: log(e^x) is NOT x if log's base = 10. e) Refactored utility functions that created artificial pileups for testing into separate class ArtificialPileupTestProvider. Right now functionality is limited (one artificial contig of 10 bp), can only specify pileups in one position with a given number of matches and mismatches to ref) but functionality will be expanded in future to cover more test cases. f) Use this utility class for IndelGenotypeLikelihoods unit test and for PoolGenotypeLikelihoods unit test (the latter testing functionality still not done). g) Linearized implementation of biallelic exact model (very simple approach, similar to diploid exact model, just abort if we're past the max value of AC distribution and below a threshold). Still need to add unit tests for this and to expand to multiallelic model. h) Update integration test md5's due to minor differences stemming from linearized exact model and better error model math
Guillermo del Angel
2012-04-27 14:41:17 -0400
da83076ab5The name still sounds silly to me, but less silly than before
Eric Banks
2012-04-27 14:39:47 -0400
959f5417f2Handle complex multi-allelic events
Eric Banks
2012-04-27 14:19:41 -0400
08bebcecbdUpdating the status values
Eric Banks
2012-04-27 14:07:48 -0400
d8f6bc232bAdding support for non-haplotype-based comparison of multi-allelics (i.e. we do compare alleles and test for partial equality, but we don't construct haplotypes for this yet).
Eric Banks
2012-04-27 13:43:52 -0400
1bbb156afaFixing compile error
Eric Banks
2012-04-27 12:52:39 -0400
0439047269Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2012-04-27 10:49:45 -0400
05b44dd017The genotypeCounts array wasn't always being initialized before it was accessed, leading to a NPE (which got caught and thrown as a JEXL expression when used in selection). Added unit test to cover all genotype count methods.
Eric Banks
2012-04-27 10:49:36 -0400
9801dd114fBug fix for: https://getsatisfaction.com/gsa/topics/problem_with_indelrealigner_and_l_unmapped The GATK -L unmapped is for GenomeLocs with SAMRecord.NO_ALIGNMENT_REFERENCE_NAME, not SAMRecord.getReadUnmappedFlag() Previously unmapped flag reads in the last bin were being printed while also seeking for the reads without a reference contig.
Khalid Shakir
2012-04-27 09:58:38 -0400
005cdcad5bMerge branch 'master' of ssh://gsa3.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Khalid Shakir
2012-04-27 09:58:14 -0400
64077ec7c8Add option to use XHMM to genotype all possible consecutive sub-segments of CNVs
Menachem Fromer
2012-04-27 01:42:20 -0400
2ad1aa2a2cMerge branch 'master' of ssh://gsa3.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Khalid Shakir
2012-04-26 19:31:47 -0400
db41d10f54First (very rough) version of a haplotype-based resolver of alleles from two provided VCF files. It works well on standard cases (e.g. MNP vs. 2 SNPs) but still needs to be tested more thoroughly and I need to add support for multi-allelics (although I know how to do that now). Being committed in private for Ryan's benefit, but no one else should be using it now.
Eric Banks
2012-04-26 16:30:22 -0400
b8c0405715Updates to the WGP to only run eval on chr20. PicardIntervals object now prints out a meaningful toString when HSP batches return multiple interval lists.
Khalid Shakir
2012-04-26 16:28:45 -0400
2f86ccb086Correct md5's for previous code change
Guillermo del Angel
2012-04-26 16:20:41 -0400
972d6531b6Corner case fix for indel GL computation: sometimes (depending on surrounding context) reads which are not informative of two candidate haplotypes end up having marginally higher likelihoods with one haplotype as opposed to another, depending on uncertainty on alignments in surrounding regions. So, a sample whose GL is -0.0001,-0.0005,-0.001 may have its genotype set to 1/1 due to this statistical noise. We already have a tolerance comparing max(gl)-min(gl) to avoid genotyping, so this tolerance is now increased from 0.001 to 0.1 (equivalent to 1 PL unit) to avoid genotyping a sample if all PLs are within this threshold. Changed 2 integration test md5s that hit this case.
Guillermo del Angel
2012-04-26 10:15:26 -0400
ab2a952ad1PED support for Inbreeding Coefficient annotation
Laurent Francioli
2012-04-25 16:51:16 +0200
219b0a128bPED support for ChromosomeCounts annotation
Laurent Francioli
2012-04-25 17:52:23 +0200
19d5213d5aAdded function to get founders IDs in SampleDB
Laurent Francioli
2012-04-25 16:27:38 +0200
120deaa010Remove old licensing
Mark DePristo
2012-04-25 12:23:08 -0400
dab25afc88Add warning message about ratios in variantQCreport, give ratio for MAF > 10%
Mark DePristo
2012-04-25 12:22:32 -0400
902277856efix for RBP getPileupsForSamples()
Mauricio Carneiro
2012-04-24 12:50:46 -0400
d6277b70d8Forgot to consider the optimized case in hasAllele
Eric Banks
2012-04-24 11:32:28 -0400
91bad244d5Using a VCF whose ALT is the reference in GGA mode is a User Error
Eric Banks
2012-04-24 11:08:37 -0400
74ad008163Adding VariantContext.hasAlternateAllele functionality
Eric Banks
2012-04-24 11:07:46 -0400
66f3315548Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2012-04-24 09:39:55 -0400
bcb93dda5fFixing docs (rank sum test values are not phred-scaled)
Eric Banks
2012-04-24 09:39:42 -0400
e39a59594aBQSR triage and test routines
Mauricio Carneiro
2012-04-20 12:59:59 -0400
a733723439Merged bug fix from Stable into Unstable
Eric Banks
2012-04-23 10:30:30 -0400
2761da975eHandle null VCs (which can arise when indels are present in the file)
Eric Banks
2012-04-23 10:30:00 -0400
cd63bcb1b8Fixing unit tests to register the user exception being thrown (instead of the NumberFormatException)
Eric Banks
2012-04-23 10:06:51 -0400
63aa79df82Slightly better error message
Eric Banks
2012-04-23 09:37:28 -0400
7b5fbf9567Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2012-04-23 09:34:08 -0400
4edb005411Catch poorly formatted PL/GL fields
Eric Banks
2012-04-23 09:33:50 -0400
35bb55f562Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-04-22 13:23:36 -0400
18e4532d10Turning down the amount of assembly graph pruning slightly in the case of low coverage.
Ryan Poplin
2012-04-22 13:23:24 -0400
10e0647347Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Menachem Fromer
2012-04-21 23:19:16 -0400
0630aa1cf0Only build valid GenomeLoc loci; throw explicit exception when sample's BAM is not found
Menachem Fromer
2012-04-21 23:18:41 -0400
1f23d99dfaIf we are subsetting alleles in the UG (either because there were too many or because some were not polymorphic), then we may need to trim the alleles (because the original VariantContext may have had to pad at the end). Thanks to Ryan for reporting this. Only one of the integration tests had even partially covered this case, so I added one that did.
Eric Banks
2012-04-20 17:00:05 -0400
4b81c75642Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2012-04-20 14:30:19 -0400
f1c5510ec0When running SelectVariants with the excludeNonVariants option, remove alleles from the ALT field that are no longer polymorphic.
Eric Banks
2012-04-20 14:30:04 -0400
a1596791afMerge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-04-20 14:03:04 -0400
a57295eb75Fixing a bug when breaking up active regions where the resulting regions would overlap by one base. Adding quality score manipulation from the UG into the haplotype caller (qual capped by mapping quality, min qual threshold).
Ryan Poplin
2012-04-20 14:02:55 -0400
40a247e860Run HC and UG for comparison; run HC with genotypeFullActiveRegion to get phased genotypes
Menachem Fromer
2012-04-20 13:33:09 -0400
aa903de892Hooking up the haplotype genotyping option requested by Menachem.
Ryan Poplin
2012-04-20 11:46:37 -0400
de68363c23Removed experimental feature (aka hack) that was meant for 1000G consensus but remained in VQSR data manager - QD was being scaled by indel length. There's no evidence any more that QD is length-dependent, neither in CEU trio data nor in latest 1000G P2 calls
Guillermo del Angel
2012-04-20 10:58:34 -0400
a1561a97c4Changing the name of the integration test (too long to type) and disabling tests during the triage...
Mauricio Carneiro
2012-04-19 20:36:35 -0400
d2488dfb81Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Guillermo del Angel
2012-04-19 19:40:03 -0400
c44c7b9a97Restored optimization in Pair HMM only to compute HMM matrices starting in index where haplotypes start to diverge - saves about 15-20% of runtime which is what we lost by disabling banding in latest version, so runtime should be now about the same as what it was before refactoring. Output is bit-true to previous commit
Guillermo del Angel
2012-04-19 19:39:43 -0400
df5dd841afAC strat now checks if evals will be merged before throwing an error on multiple eval files. Minor tweaks to WGP script based on new recal VCF format.
Khalid Shakir
2012-04-19 16:08:55 -0400
3fa9089085Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Guillermo del Angel
2012-04-19 14:37:34 -0400
6d5b05c123Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Menachem Fromer
2012-04-19 14:18:34 -0400
53ebde2c3bAdded Queue script to run HaplotypeCaller on user-defined sets of samples at particular loci
Menachem Fromer
2012-04-19 14:17:57 -0400
1ae2ab5b63Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Guillermo del Angel
2012-04-19 12:50:29 -0400
0e6e0cb907Merging bug fixes
Guillermo del Angel
2012-04-19 12:49:30 -0400
79272c5e15Thanks to Menachem for pointing out that the docs for genotyping_mode and output_mode were the same (and unclear). Fixed.
Eric Banks
2012-04-19 12:48:09 -0400
02ff930f6aMy changes
Guillermo del Angel
2012-04-19 12:45:18 -0400
2485cef5b8Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Eric Banks
2012-04-19 11:46:06 -0400
76a6e37f4fDon't output callability metrics by default anymore; one can still have them output to the 'metrics' file (which is now @Hidden because they are really for GSA use). Added a TODO to move UG from @By reference to reads and rods once LIBS is cleaned up.
Eric Banks
2012-04-19 11:45:56 -0400
1ea4e48a27Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-04-19 11:32:32 -0400
11001ab9a2Adding option to HaplotypeCaller to genotype the events on the chosen haplotypes as independent events. The filtered reads are now kept around so they can be passed to the variant annotations. Unfortunately the filtered reads aren't assigned a likelihood yet so they are all thrown in the Allele.NO_CALL bin.
Ryan Poplin
2012-04-19 11:32:10 -0400
eb22cd7222Unit test to guarantee BQSR sequential calculation accuracy
Mauricio Carneiro
2012-04-18 23:02:10 -0400
68d0211fa1Improved BQSR plotting and some new parameters
Mauricio Carneiro
2012-04-18 13:02:41 -0400
143e92b797Rebasing
Guillermo del Angel
2012-04-11 13:56:51 -0400
a530127956More merge bug fixes
Guillermo del Angel
2012-04-18 19:59:39 -0400
960e7e6aafChanges to integration tests
Guillermo del Angel
2012-04-18 19:53:42 -0400
82efd4457eRevert some bad merge changes
Guillermo del Angel
2012-04-18 16:35:09 -0400
31c394d588Resolve merge conflicts
Guillermo del Angel
2012-04-18 16:25:03 -0400
4999ae87adMerge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Ryan Poplin
2012-04-18 15:02:42 -0400
dcc4871468minor misc optimizations to PairHMM
Ryan Poplin
2012-04-18 15:02:26 -0400
673fc00343Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Menachem Fromer
2012-04-18 14:17:00 -0400
66d3fec8e2Need to print newline in printf
Menachem Fromer
2012-04-18 14:15:50 -0400
Joel Thibault
Mark DePristo
David Roazen
Eric Banks
Mauricio Carneiro
Guillermo del Angel
Christopher Hartl
Ryan Poplin
Khalid Shakir
Menachem Fromer
Laurent Francioli