ec68ae3bc5
Added a filter that will split the read set by a threshold of mapping quality (Request from Jason Flannick)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1812 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-12 20:58:37 +00:00
0d73fe69e7
Recalibrator by NQS. Had this puppy running all afternoon. Thing had got through 100,000,000 reads before I decided to delete my sting tree. *sigh*, a little more delay.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1811 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-12 20:55:02 +00:00
ee0afba0af
Recalibration stuff...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1810 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-12 20:51:39 +00:00
62c484b57a
Fixes for GSA-201, where enumerated types in command line arguments had to be defined as all uppercase for the system to work.
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Also a little playground walker that changes the sort order flag of a BAM file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1805 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-09 18:11:32 +00:00
d9f5a314ac
avoid an out of memory error by no putting more than 5000 reads in the cache. on pilot1 at least those are crazy loci anyway.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1802 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-09 14:56:55 +00:00
6d7f4481e4
Changed traversal type slightly
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1800 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-09 04:11:48 +00:00
a9f3d46fa8
Your time has come, SSG.
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Fare thee well.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1799 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 20:27:56 +00:00
8fdb8922b8
now output in the exact format that works with sequenom software.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1798 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 20:06:27 +00:00
98e3a0bf1a
VCF can now be emitted from SSG. The basic's are there (the genotype, read depth, our error estimate), but more fields need to be added for each record as nessasary.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1797 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 19:50:04 +00:00
94d82d1915
Matthew Bainbridge's duplicate removal utility for 454 data. This code should eventually be moved into a read walker. For now, it's being introduced into the repository as-is (well, with one minor change to make the handling of command-line arguments a little more straightforward).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1794 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 18:32:37 +00:00
f89a89ffe3
Use of AlleleFrequency as an input to PowerAndCoverage is deprecated by the new walker. Reverting to the standard "power at 1 allele" calculation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1788 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 16:07:45 +00:00
ae05f5c7ad
Fixin the header.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1787 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 15:49:28 +00:00
11ff1e09b8
A new power walker for the user to feed in a number of alleles. Call that number k. Output is:
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Locus Power_for_k_alleles Power_for_k-2_alleles Power_for_k-2_alleles ... Power_for_1_allele
This was a request from Jason Flannick & the T2DB group.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1786 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 15:35:35 +00:00
32128e093a
misc. changes to get the numbers back to the baseline while keeping the speedup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1784 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 12:27:07 +00:00
d38a0d04b9
fix a snp mask offset error.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1783 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 12:25:40 +00:00
02d2492d68
Simple tool for picking sequenom probes for SNPs. Can be extended to indels if necessary.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1780 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-07 23:46:41 +00:00
5bdcc2b4dc
Included HLA class 2 genes in CreatePedFileWalker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1776 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-07 18:46:51 +00:00
8f896b734f
Included HLA class 2 genes in CreatePedFileWalker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1775 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-07 18:28:01 +00:00
225b9bccc1
Modifications to NQSClusteredZScoreWalker to output empirical mismatch rates on bins by both Z-score and reported Q-score, rather than averaging over all Q-score bins for each Z-score.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1773 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-07 13:45:12 +00:00
8dd0924b37
Minor performance improvements to VariantEval -- now all of the CPU time is spent dealing with the ROD system...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1772 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-06 23:40:30 +00:00
3aec76136f
Removing the AllelicVariant interface, which is replaced by the Variation interface.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1770 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-06 17:44:24 +00:00
1bd0c3c145
variant eval allows non Variation rod objects
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1768 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-06 13:04:26 +00:00
98076db6b4
Modified CreatePedFileWalker to output PED file given HLA allele names
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1763 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-05 03:06:42 +00:00
7605ee500c
Idiocy! All tests were being disabled because I forgot the instanceof
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1760 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-02 20:04:56 +00:00
88d0890cc3
Made PooledGenotypeConcordance a standard test in VariantEval
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1759 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-02 20:03:31 +00:00
68cb2ee54b
Tweaks to parameters for NQS analysis walkers; change to PowerAndCoverage for Jason Flannick (can input the number of alleles to compute power for - i.e. doubletons, tripletons; rather than statically checking singletons.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1757 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-02 19:11:27 +00:00
e885cc4b21
changes for corrected GLF likelihood output, along with better tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1754 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-01 20:45:05 +00:00
2309d19f6f
Bug fix from Michael Ross: mark second read in sequence as second of pair.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1753 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-01 14:34:36 +00:00
b1c321f161
Adjusted Genotype concordance to more accurately use the new Genotyping code, fixed the VCF rod, and temp. fix the build by reintroducing Shermans ReadCigarFormatter
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1745 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-29 21:28:21 +00:00
9b78a789e2
HLA Caller 2.0 Walkers:
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CalculateBaseLikelihoodsWalker.java walks through reads calculates likelihoods using SSG at each base position
CalculateAlleleLikelihoodsWalker.java walks through HLA dictionary and calculates likelihoods for allele pairs given output of CalculateBaseLikelihoodsWalker.java
CalculatePhaseLikelihoodsWalker.java walks through reads and calculates likelihoods score for allele pairs given phase information
File Readers:
BaseLikelihoodsFileReader.java reads text file of likelihoods outputted by SSG
FrequencyFileReader.java reads text file of HLA allele frequencies
PolymorphicSitesFileReader.java reads text file of polymorphic sites in the HLA dictionary
SAMFileReader.java reads a sam file (used to read HLA dictionary when in another walker)
SimilarityFileReader.java reads a text file of how similar each read is to the closest HLA allele (used to filter misaligned reads)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1744 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-29 20:45:55 +00:00
281a77c981
Bugfix. isMismatch() was actually computing isMatch().
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1743 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-29 20:04:59 +00:00
e28b45688c
More NQS Related Walkers to play with
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1742 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-29 20:01:04 +00:00
6134f49e3c
Convert de novo SNP caller to run using parent1 and parent2 BAM files (by splitting contexts by reader using getMergedReadGroupsByReaders) instead of geli files providing a large speed-up and obviating the need for large whole-genome geli files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1738 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-29 06:42:21 +00:00
5662a88ee1
Cosmetic change to list sampling functions: the typical usage of n and k were reversed. No change in functionality of the classes has been made and unit tests still pass.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1736 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-28 18:12:32 +00:00
39598f1f0a
switching the concordance walker over to the new Variation system
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1735 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-28 15:46:36 +00:00
92c6efabb7
moving IndelGenotyper out of playground
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1732 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-25 19:44:49 +00:00
fe6d810515
Some basic commits that I've been sitting on for a while now:
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@ PooledGenotypeConcordance - changes to output, now also reports false-negatives and false-positives as interesting sites. It's been like this in my directory for ages, just never committed.
@NQSExtendedGroupsCovariantWalker - change for formatting.
@NQSTabularDistributionWalker - breaks out the full (window_size)-dimensional empirical error rate distribution by the window. So if you've got a window of size 3; the quality score sequences 22 25 23 and 22 25 24 have their own bins (each of the 40^3 sequences get one) for match and mismatch counts.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1730 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-25 19:35:50 +00:00
f7684d9e1b
ImputeAllelesWalker fills missing portions of HLA dictionary based on best allele matches
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1729 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-25 18:51:46 +00:00
235de38c2e
Updates to FindClosestAlleleWalker and CreateHaplotypesWalker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1728 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-25 16:41:58 +00:00
7ffc1d97ef
Cut DeNovoSNPWalker over to the new Variation system, some renaming of methods on the Variation interface, and some corrections on the interface.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1724 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-25 04:35:52 +00:00
392152f149
1000x performance improvements to MSG for crisis control
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1723 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-24 23:44:33 +00:00
d262cbd41c
changes to add VCF to the rod system, fix VCF output in VariantsToVCF, and some other minor changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1715 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-24 15:16:11 +00:00
1ee8ba590c
Reads cigar files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1713 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-24 03:14:10 +00:00
9422156e09
Finds closest allele for each read in bam file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1712 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-24 03:12:20 +00:00
5c5151c4e7
Creates ped file from reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1711 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-24 02:48:29 +00:00
b446b3f1b6
CreateHaplotypeWalker now gives correct output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1709 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-23 21:13:52 +00:00
3916e165fb
New walker to output haplotypes for each read (for SNP analysis or imputation, etc)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1707 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-23 20:26:43 +00:00
63f3d45ca4
fixing the build
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1705 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-23 20:04:09 +00:00
540e1b971f
And we fix one boneheaded mistake, which was actually causing the problem; though the last change was still correct.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1704 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-23 19:26:45 +00:00
124ca68fa8
And an IMMEDIATE minor fix (want neighborhood quality > base quality to be represented correctly)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1703 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-23 19:21:09 +00:00
chartl
aaron
jmaguire
ebanks
kiran
sjia
depristo
hanna
andrewk
asivache