11aa715630
added capability for filtering by platform
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1011 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 19:19:50 +00:00
8f4bc8cb6e
Move filtering functionality into the PrintReadsWalker. More to come.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1010 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 16:38:08 +00:00
161c74716c
Forgot to change some direct references to variables in SSG. Fixed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1009 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 14:16:18 +00:00
9eeb5f79d4
Various refactoring to achieve hapmap and dbsnp awareness, the ability to set pop-gen and secondary base priors from the command-line, and general code cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1008 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 07:21:08 +00:00
f2946fa3e8
Various refactoring to achieve hapmap and dbsnp awareness, the ability to set pop-gen and secondary base priors from the command-line, and general code cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1007 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 07:20:22 +00:00
f6af190b74
ignore clipped reads for realigning indel positions
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1006 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 01:01:27 +00:00
0583459839
Another formatting change to make Hapmap sites more clearly visible.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1004 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-12 19:53:21 +00:00
811f560efb
add refseq annotations to single sample calls
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1003 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-12 19:43:30 +00:00
e9be2a9c60
Changed a formatting issue.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1002 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-12 19:40:32 +00:00
ca09a10b76
refseq annotation rod is now manually bound to tell coding indels from non-coding ones
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1001 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-12 19:27:37 +00:00
5859948e80
Fixed bugs in CleanedReadInjector arising from integration testing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@999 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-12 17:37:33 +00:00
fb7ba47fff
Now does really neightbor distance calculation, as well as true snp cluster counting
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@998 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-12 16:29:26 +00:00
dbf2cc037c
don't have a null-pointer hissy fit when the reference is N.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@997 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-12 13:59:16 +00:00
4eda040e0f
what used to be internal cutoff values are now exposed as cmdline parameters: minCoverage, minNormalCoverage, minFraction, minConsensusFraction
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@995 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 21:22:52 +00:00
41687d5237
Added accessors for the prior probabilities.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@994 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 21:16:10 +00:00
12dd18cdba
Now aware of Hapmap and dbSNP sites. We *can* change the priors there, but we don't yet.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@993 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 21:15:34 +00:00
d5cd883b99
bug fixed when a read with alignment end exactly at the window boundary and with last cigar element being an indel would cause index-out-of-bounds exception
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@992 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 21:03:15 +00:00
a12009e9e7
Added a new constructor in which priors for hom-ref, het, and hom-var can be specified. Otherwise, it uses the default values of 0.999, 1e-3, and 1e-5 respectively.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@991 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 20:33:45 +00:00
909fefa40a
Argumentized priors for hom-ref, het, and hom-var.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@990 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 20:32:44 +00:00
71e3825fa1
First pass of a walker for Eric that searches through an input BAM file for unclean reads, injecting the cleaned reads in their place and outputting the composite result.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@989 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 20:18:13 +00:00
032d0436e6
Added ROD for 1KG SNP calls
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@988 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 19:53:51 +00:00
ffffe3b2f6
-Support for 1KG SNP calls in RODs
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-Minor bug fix
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@987 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 18:56:37 +00:00
63b5c12cbd
Changed dataSources to datasources, to be consistant with the rest of our package names. Also, this makes me champion in the largest check-in contest.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@985 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 18:13:22 +00:00
195b4ea7b4
a rename for consistancy of Sam to SAM, creating a genotype utils dir, and moving the GLF code into it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@984 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 17:46:06 +00:00
599ceeddd8
Better method for downsampling deep regions
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@983 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 16:57:40 +00:00
4d9a88153a
Update inferred insert size of cleaned reads when they are paired
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@982 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 16:29:13 +00:00
3796654069
Added walker to emit intervals of clustered SNP calls
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@981 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 00:57:14 +00:00
678ddd914f
Stopgap fixes GFF, DbSNP being half-open rather than half-closed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@980 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 21:38:57 +00:00
94b0e46d12
checked in a sample xml file used to store the defaults for the SomaticCoverage tool, and added it to the SomaticCoverage.jar in build.sml. Also added a inputStream marshalling method to the GATKArgumentCollection.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@979 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 20:46:16 +00:00
8d25f1a105
should be a little faster
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@978 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 20:33:45 +00:00
026f68fb41
a couple of quick name changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@976 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 20:02:52 +00:00
72a81f8f25
removed the requirement that a bam file list be present in the XML version of the command line arguments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@975 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 20:01:13 +00:00
b1f90635c1
1. downsample when there are too many mismatching reads (needs perfecting)
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2. allow user to specify that no reads be emitted
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@974 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 19:55:42 +00:00
39dcd4f11f
an attempt to bail out when unmapped reads are reached at the end of the file(s). still testing...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@973 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 19:53:50 +00:00
030efc468f
added naive ad-hoc cutoff for the pile size the cleaner will attempt to process; use --maxPileSize argument to force any pile larger than specified cutoff to be directly written to the output without cleaning
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@972 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 17:52:35 +00:00
f9be175f44
Be smart about trying alternate consenses:
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try prior indels first and only 1 instance of them
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@971 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 17:43:22 +00:00
f304803811
initial check-in of an easy way to create command line tools based on the GATK
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@970 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 17:34:02 +00:00
b0cc763eb5
Added some methods to format bases such that read bases on the forward strand are in uppercase, while those on the negative strand are lowercase. This does *not* affect the default functionality of the standard PileupWalker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@969 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 17:31:00 +00:00
9ebcd6546d
Convenience printing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@968 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 17:07:38 +00:00
06e5a765f8
now has two modes: one sample - just call indel sites; two samples - call somatic-looking variants only. Still uses heuristic count-based cutoffs, cutoffs are hardcoded and are pretty conservative...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@967 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 16:41:38 +00:00
5451bbfd5a
-move final vars to command-line args
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-Per Andrey: ignore indels from aligner when testing against alt consensus
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@966 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 16:39:00 +00:00
ad80894afa
Bumped picard to latest svn version.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@965 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 14:36:34 +00:00
ec2f015447
fixed a bunch of comments and license headers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@964 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 14:10:46 +00:00
6bb7f7e9d8
Commented some stuff out so that things compile.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@963 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 14:06:33 +00:00
dc6a9ca196
Pooling resources to lower memory consumption.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@962 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 13:39:32 +00:00
87ba8b3451
Removed some useless code. Don't apply second-base test if the coverage is too high, since the binomial probs explode and return NaN or Infinite values.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@961 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 08:27:06 +00:00
a12ed404ce
Changed method name from applyFourBaseDistributionPrior to applySecondBaseDistributionPrior. 'Cause that's how I roll.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@960 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 08:21:22 +00:00
3adb4239e4
Same as regular Pileup, but also allows you to see flanking region around locus. This will be useful in determining that some SNPs are spurious due to being at the ends of homopolymer regions.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@959 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 08:19:31 +00:00
2b0e7f612b
Handles bam pileups where some of the reads have SQ tags and some don't.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@958 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 08:17:15 +00:00
36c98b9d6c
added tools to test read based traversals using the artificial in-memory SAM file tools, and testing of the PrintReadsWalker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@957 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 01:52:25 +00:00
ebanks
kiran
asivache
hanna
depristo
jmaguire
aaron