4e0cd6ab84
Now works on single samples and computes metrics.
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Here is an example metrics output from a very tiny region:
Allele Frequency Metrics (LOD >= 5)
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Total loci : 14704
Total called with confidence : 10920 (74.27%)
Number of Variants : 16 (0.15%) (1/682)
Fraction of variant sites in dbSNP : 100.00%
Missing:
Microarray(hapmap) concordance, tp/fp.
Optional:
Histograms of depth of coverage, LOD, observed allele frequency, etc.
Still to implement:
Propagate command line argument N (number of chromosomes) into walker to enable pooled calling.
Take allele frequency priors as input.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@133 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-22 15:45:12 +00:00
1fcf4c0cbf
Update picard to work with new samtools.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@123 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-20 21:51:26 +00:00
5dca560c3c
A bunch of refactoring, and more on the way.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@122 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-20 21:31:07 +00:00
c5433a3120
dumps out base qualities per position for use in making boxplots
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@119 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-20 17:01:18 +00:00
f3f1b47808
deal with reverse complemented reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@115 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-20 16:01:49 +00:00
6bcdac5c62
Restructured AlleleFrequency classes into 3 classes: AlleleFrequencyWalker, AlleleFrequencyMetricsWalker, AlleleFrequencyEstimate. AlleleFrequencyMetricsWalker class now calls mapper function of AlleleFrequencyWalker and works with the result. AlleleFrequencyEstimate is now a separate class instead of a subclass of AlleleFrequencyWalker.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@102 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-19 22:06:01 +00:00
5fa99f430e
One line format is useable and two levels of debug output are available (debug = 1: one line format, debug = 2: table of sampled probs for each locus). Class AlleleFrequencyMetrics computes %dbSNP and frequency of SNPs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@99 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-19 15:05:05 +00:00
225ea64bd9
Moved extra walkers at Mark's request.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@96 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-18 23:52:08 +00:00
ffb6f8f5da
Move the basic gatk framework into the core subtree.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@95 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-18 23:39:00 +00:00
45d2a9acd8
Added walker to print out a histogram of where mismatches occur in alignments
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@89 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-18 19:46:42 +00:00
d46ee96269
Added support for loose Walker class files in walkers directory.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@87 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-18 17:32:24 +00:00
fe9e52c47e
allow on fly sorting AND validation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@86 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-18 15:50:17 +00:00
bb94c853f8
Added WalkerManager -- a class that dynamically loads available walkers
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from the jar file. For now, added placeholder Walker interface so that
WalkerManager could work with classes of type Walker rather than classes
of type Object.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@85 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-17 23:22:37 +00:00
d9fa04f65c
Fixed logic
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@84 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-17 22:20:03 +00:00
1aa3958644
Added ability to sort reads on the fly
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@83 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-17 20:29:09 +00:00
58aa2aab43
Rough draft of patch to use bam indices when available.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@81 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-17 16:39:03 +00:00
478425b3d8
Better error messages
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@79 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-17 15:37:02 +00:00
0fd55d91d2
Fixed bug in unsafe mode
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@78 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-17 15:28:04 +00:00
c74bd871b1
added module for aligned reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@77 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-17 14:08:54 +00:00
28cc670a92
Walker to print out a histogram of aligned reads per mismatches allowed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@76 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-17 14:05:29 +00:00
9ae551e858
Lots of error checking added, fixed bugs associated with reading files out of order, added support for U (unsafe) flag for processing reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@75 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 23:22:04 +00:00
34d9af4702
Remove orphaned modules directory.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@67 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 21:53:05 +00:00
685fc8bd61
Partial implementation of single sample allele calling
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@64 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 19:30:42 +00:00
8ccbcc4101
Mismatch counter
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@62 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 15:51:48 +00:00
3b5003bd11
Added support for accessing the reference in read traversal
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@60 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-16 14:46:19 +00:00
69aa669928
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@56 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-15 22:42:24 +00:00
01e950ef2f
Reference ordered data files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@55 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-15 22:37:20 +00:00
24ae381c97
Renaming of ATK to GATK, the genome analysis TK.
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Also added several more layers of error checking
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@54 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-15 22:23:25 +00:00
c9cb7a3596
Renaming of ATK to GATK, the genome analysis TK.
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Also added several more layers of error checking
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@53 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-15 22:21:48 +00:00
jmaguire
hanna
ebanks
andrewk
depristo