8bcbf7f18a
First draft of multi sample caller accuracy test.
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Doesn't do it's job yet but the pieces are in place.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1170 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-05 16:29:13 +00:00
4019cd2bd7
Added ROD for parsing hapmap3 genotype files.
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Tweak to TabularROD to allow HapMapGenotypeROD to work.
Added HapMapGenotypeROD to list of RODs in ReferenceOrderedData.java.
Modified MultiSampleCaller to return a single object with most of the relvant information.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1169 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-05 16:28:24 +00:00
be2f8478c0
added supression of failure messages
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1164 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-03 15:19:37 +00:00
25c30b12bb
added MAF-style output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1163 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-03 15:10:19 +00:00
dcb8892568
Lot of code for coverage evaluation tools including first version of python script to evaluate the downsampled SSG callls made and the java code to make all the calls at Hapmap chip sites at various downsampling levels; ListUtils contains functions for randomnly subsetting lists (with replacement) which are useful for subsetting the same elements in both the reads and the offsets lists of a LocusWalker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1162 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-03 08:07:02 +00:00
d603145cb0
Meaning of input arguments has CHANGED: minFraction is now a minimum fraction of CONSENSUS indel observation, out of all reads covering the site, required to make the call. minConsensusFraction is still the minimum fraction of CONSENSUS indel observation out of all indel observations at the site
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1160 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-02 20:38:10 +00:00
6a25f0b9c5
refactored into new package
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1158 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-02 14:37:54 +00:00
c2e5a68aaf
output format changed in --verbose --somatic mode: now also prints the <#reads with indels>/<coverage> for normal samples, rather than only for the tumor; also, code cleaned up a little
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1149 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 20:56:16 +00:00
4cbf069de1
First version of coverage evaluation tool
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1148 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 20:52:25 +00:00
76fd4b3848
deal with different contigs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1146 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 19:17:27 +00:00
20fab507a8
Choose the REF if it scores equal to consensus!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1145 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 18:54:27 +00:00
5a5103cfd2
Heads up, everyone: command-line args no longer need to be public.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1143 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 16:09:22 +00:00
93da64db10
Update naming for consistency.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1136 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 22:03:21 +00:00
8d3dc57c3d
Commit to emit in sorted order so we don't have to use /tmp
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1133 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 19:47:15 +00:00
f5cba5a6bb
Fixed genome loc to be immutable, the only way to now change it's values is through the GenomeLocParser.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1132 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 19:17:24 +00:00
08df4771c8
count X/N/etc. as mismatches for the NM attribute in the BAMs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1127 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 16:08:55 +00:00
d412c5dc2f
Updated to use SecondaryBaseAnnotator class.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1126 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 16:08:43 +00:00
8aa3b65e7f
fix to guarantee emission in sorted order
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1122 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 13:48:41 +00:00
a17bf145f6
fix to respond to the change in IndelLikelihood constructor.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1119 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-29 19:05:33 +00:00
95e2ae0171
Deal with reads whose ends are aligned off the end of a chromosome.
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Includes update to ignore non-ATCG bases (not just 'N')
(Also, create a BWA dir for future work)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1117 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-29 16:50:05 +00:00
65a788f18a
Added a ROD (SangerSNP) for parsing the Sanger's chr20 pilot1 SNP calls.
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Some doodling around with indel calling in an EM context.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1116 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-29 16:32:12 +00:00
ceeeec13b8
Computes a vector of numbers of reads falling into successive intervals of specified length (e.g. numbers of reads per every 1Mbase)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1115 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-29 16:12:21 +00:00
eb74b16e39
updated what constitutes removing entropy
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1113 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-26 18:29:00 +00:00
1a97c86f95
don't crash when an unmapped read is encountered, just write it into the output file, it should be ok
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1111 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-26 15:33:59 +00:00
5289230eb8
Version 0.2.1 (released) of the TableRecalibrator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1108 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 22:50:55 +00:00
73caf5db15
This is, strictly speaking, NOT a GATK module. Standalone, picard-level executable except that it uses couple of gatk utils (GenomeLoc). Remaps alignments from cutom reference (such as transcritome, hyb-sel etc) onto the 'master' reference
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1107 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 22:04:18 +00:00
ad3a3aa350
First pass at passing lists of files / lists of interval arguments work. Note that the interval
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ROD system will throw up its hands and not deal with intervals at all if multiple interval files
are passed in (see JIRA GSA-95).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1105 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 20:44:23 +00:00
0c3aabd1c5
logger output should be less verbose by default. Also fixed a printout in my read validation walker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1102 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 19:47:29 +00:00
11d83ac7d0
pushing up to test on unix box
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1101 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 19:00:48 +00:00
0d9041380d
remove printouts
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1100 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 18:54:14 +00:00
2c97c5e873
Compute a simple histogram of depth of coverage.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1098 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 18:30:11 +00:00
3b24264c2b
incorporating skew check, further output of metrics
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1094 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 16:01:07 +00:00
940d75171a
Big cleaner changes:
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1. Added a Walker to merge intervals before cleaning
2. (Almost) all Walkers can filter out 454 reads (and do by default)
3. Got rid of -all command and related pieces (time to switch to CleanedReadsInjector)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1090 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 14:31:24 +00:00
3cb6d7048e
don't freak out if two reference intervals a custom contig is built of are strictly adjacent; instead politely warn user that her data suck and proceed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1089 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-24 19:08:10 +00:00
d4f3ca1a10
A utility class for keeping the mapping from 'custom' reference (e.g. transcriptome) onto the 'master' reference (e.g. whole genome), and for remapping SAM records from the former onto the latter. It's Arachne's BaitMultiMap, pretty much
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1088 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-24 18:16:15 +00:00
69dc502174
I forgot that this depends on BoundedScoringSet.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1087 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-24 17:18:53 +00:00
a9c30c5fcc
added -nosort cmdline flag; if specified, the output writer does not attempt to sort reads on the fly (sorting involves use of sorting collection backed up by temporary disk storage and can lead to crashes if temp size is low and/or filesystem is not behaving). Output can be later sorted externally by samtools
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1085 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-24 15:58:00 +00:00
3112302ec9
A priority-queue-like container that allows you to add a specified number of elements. When the limit has been reached, new additions replace the lower scoring elements.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1083 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-24 15:39:47 +00:00
dfa2efbcf5
not crashing when refseq annotation track is not requested is a nice added feature
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1079 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-23 22:52:40 +00:00
eb999f880a
incorporating skew check
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1078 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-23 19:51:51 +00:00
1339f3f3e3
make refseq annotation file an optional argument; if specified, indels will be annotated as genomic/utr/intron/coding (accidentally appearing 'unknowns' probably mean that there's something wrong with refseq annotations?)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1077 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-23 18:17:03 +00:00
9c0dba6979
Some quick documentation and typo changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1076 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-23 13:40:13 +00:00
cb9c6f18ef
spelling fix
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1074 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-23 01:46:35 +00:00
630d9e6a37
Fixed a typo.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1073 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-22 21:37:46 +00:00
8b4d0412ca
Changed the duplicate traversal over to the new style of traversal and plumbed into the genome analysis engine. Also added a CountDuplicates walker, to validate the engine.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1072 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-22 21:11:18 +00:00
9e25229014
use better entropy threshold and don't print out "new" SNPs (since they're just an antrifact of the low (arbitrary) threshold
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1070 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-22 15:30:08 +00:00
bcb64d92e9
Aaron: 1, GenomeLoc: 0. I changed our GenomeLoc class, seperating the creation of a genome loc (with the reference setup) to a parser class. GenomeLoc now just represents the actual genomic postion. The constructors are now package-protected (to enforce using the parser), but we may want to expose some constructors in the future.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1069 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-22 14:39:41 +00:00
26eb362f52
Added novel / known split to variant eval. That is, emits all of the standard analyses on SNP partitioned into those known in the provided known db and those novel. Also fixed problem with counting bases within subsets
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1068 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-21 21:27:40 +00:00
a21c2a7e48
don't make mapping quality too high
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1066 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-21 04:51:42 +00:00
686c8133ed
massive change in the way the cleaner works, mostly revolving around the fact
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that we no longer trust indels from the alignments (although we do use it as
a good alternate consensus possibility).
Other changes include better "greedy mode" performance and allowing the user
to have just the cleaned reads themselves be printed out (mostly for Matt's
CleanedReadInjector).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1065 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-21 03:56:59 +00:00
dde52e33eb
Cleanup of the cleaned read injector based on Eric's feedback.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1062 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-19 22:04:47 +00:00
a0a3cf2f9f
VariantFiltrationWalker can now apply specified exclusion tests after the feature tests. For a given variant, all reasons for exclusions are printed to screen.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1061 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-19 21:12:01 +00:00
58b132ee10
Eliminate redundant computation.
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Still room for more optimization, but I called chr20 (60Mb) in a couple hours on the queue this morning.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1058 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-19 16:31:57 +00:00
3a1b58ca65
remove unused argument lodThreshold.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1057 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-19 12:40:12 +00:00
9a0151b7e1
Added an option to list all available feature classes and exit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1056 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-19 00:00:12 +00:00
ed7afd8b70
Added javadocs. Now throws an exception if an unknown feature is specified. General cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1055 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 23:28:38 +00:00
284fd6a5fb
VariantFiltrationWalker now inspects its parent package and determines the list of features that can be applied. Command-line specification of filters to run look at the simple names of these features and do a case-insensitive match to determine which features to apply. A new verbose mode allows the user to see how the likelihoods are changing with the application of each subsequent feature.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1054 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 22:45:36 +00:00
af7a759ba4
Convert the somatic coverage tool to output from the packaging tool rather than from the dist target.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1050 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 21:29:30 +00:00
1bca144119
Moving things around
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1049 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 21:06:46 +00:00
ca8a3bd85e
Another temp checking for rearranging things
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1048 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 21:04:36 +00:00
a4fa02f11c
Moved output outside of for loop so I don't have 10 different versions of the same variant (though, now that I think of it, that's not necessarily a terrible thing for debugging...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1045 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 19:59:26 +00:00
768a16e791
An experimental, tile-parallel version of the secondary base annotator.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1044 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 19:58:09 +00:00
e26df45e8e
Different features can now be specified by repeatedly supplying the -F "featurename:arguments" option.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1043 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 18:45:03 +00:00
7a921c908c
Can now adjust the genotype likelihoods of a variant returned from the rod. This automatically causes the lodBtr, lodBtnb, and genotype to be recomputed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1041 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 07:26:37 +00:00
9a7cec7d2e
Directory to house variant calling and filtration tools.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1040 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 07:20:38 +00:00
5992d88409
skip N's in the reference (rather than crash. doh!)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1039 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 23:22:35 +00:00
9ef391706c
Added outputting of genotype posteriors to geli.calls file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1035 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 21:31:46 +00:00
615572ea06
output to out... not System.out...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1034 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 20:43:10 +00:00
673205ed5f
additional output tweaking
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1028 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 15:37:38 +00:00
7d281296a7
Finishing checking for building
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1027 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 14:12:40 +00:00
d1e25bfe88
Intermediate checkin for safety -- now compiles
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1026 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 13:16:55 +00:00
2250769a42
Intermediate checkin for safety -- do not use
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1025 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 13:07:19 +00:00
86c8c08375
Intermediate checkin for safety -- do not use
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1024 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 13:06:24 +00:00
6ee64c7e43
added changes to support alec toUnmappedRead seek. Huge improvements (orders of magnitude) in unmapped read performance.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1021 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-16 22:15:56 +00:00
4f6d26849f
Behold MultiSampleCaller!
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Complete re-write of PoolCaller algorithm, now basically beta quality code.
Improvements over PoolCaller include:
- more correct strand test
- fractional counts from genotypes (which means no individual lod threshold needed)
- signifigantly cleaner code; first beta-quality code I've written since BaitDesigner so long ago.
- faster, less likely to crash!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1020 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-16 20:03:24 +00:00
b11c5a7cd5
doing some read validation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1018 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-16 19:25:43 +00:00
010304fe44
bug: printing incorrect coordinates into output, finally fixed (?)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1017 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-16 18:08:56 +00:00
2259dc3a8f
added filtering out indels with large levels of noise (mismatches) remaining in the close proximity; also a bug in recording deletion coordinates is fixed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1014 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 21:13:28 +00:00
a6477df6d1
Now optionally outputs whether "SNPs" are maintained/cleaned out/introduced by cleaning
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1013 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 20:02:02 +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
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
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
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
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
jmaguire
kcibul
andrewk
asivache
ebanks
hanna
aaron
kiran
depristo