9b1d7921e8
added filter based on concordance to another call set
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1432 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-18 15:16:30 +00:00
b2a18a9d61
- first pass at a basic indel filter (for now, based on size and homopolymer runs)
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- fix simple indel rod printout
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1431 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-18 03:04:12 +00:00
78439f7305
Modify Sequenom input format based on official documentation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1430 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-18 01:42:57 +00:00
d4808433a1
Added option to output the locations of indels in the alternate reference
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1424 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-16 03:46:36 +00:00
4b6ddc55bd
Merge our 2 fastq writers into 1: incorporate Kiran's secondary-base file writer into the fasta/fastq writers
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1423 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-14 20:55:23 +00:00
0ec581080c
Refactoring the code; also, now it prints continuously instead of potentially storing one long string.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1421 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-13 01:32:46 +00:00
2a01e71277
A very simple standalone filter for fooling around with the data: can extract only mapped or only unmapped reads, only reads with mapping quals > X, reads with average base qual > Y, reads with min base qual > Z, reads with edit distance from the ref > MIN and/or < MAX
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1420 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-12 20:28:51 +00:00
ebec0ec171
A standalone companion to BamToFastqWalker: does the same thing but without calling in gatk's heavy artillery (does not "require" a reference either). Extracts seqs and quals and places them into fastq; along the way it also reverse complements reads that align to the negative strand (so that fastq contains reads as they come from the machine).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1419 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-12 20:24:37 +00:00
112a283f54
be nice, don't forget to close the reader when done
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1418 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-12 20:19:56 +00:00
ba2a3d8a58
Reverse qualities when read seq. is reverse complemented
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1417 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-12 20:17:35 +00:00
143f8eea4e
option to output in sequenom input format
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1415 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-12 16:50:37 +00:00
7f1159b6a9
Added option to mask out SNP sites with "N"s in the new reference.
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This is useful when producing Sequenom input files for validating indels...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1414 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-12 15:17:45 +00:00
43f63b7530
Added a walker to convert a bam file to fastq format (including the option to re-reverse the negative strand reads).
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Picard has such a tool but it is geared towards their pipeline and requires intimate knowledge of the lanes/flowcells,etc. This is just easy.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1413 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-12 15:10:40 +00:00
e4acd14675
Now GenomicMap maps (and RemapAlignment outputs) regions between intervals on the master reference as 'N' cigar elements, not 'D'. 'D' is now used only for bona fide deletions.
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Also: do not die if alignment record does not have NM tags (but mapping quality will not be recomputed after remapping/reducing for the lack of required data)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1411 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-11 21:10:17 +00:00
5fab934f4e
- moved the reference maker to its own directory
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- added first version of a more complicated reference maker which takes in RODs and creates an alternative reference based on the variants (indels and/or SNPs)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1409 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-11 18:01:06 +00:00
1851613de4
Now using larger database of HLA alleles
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1405 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-11 03:11:14 +00:00
3208eaabcc
A standalone picard-level tool for breaking individual reads into "pairs" of first/last N bases. Supports:
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* splitting off only start or end of the read, or both; the output will contain
chopped sequences AND corresponding base qualities
* splitting arbitrary number of bases off each end (different numbers
for left and right segments can be specified; segments can overlap)
* splitting only unmapped reads, ignoring mapped ones
* writing splitted ends into separate sam/bam files, or into a single output file
* decorating original read names with user-specified suffixes for each end
(e.g. _1 and _2 for left and right parts of the read); default: no decoration,
original read names are used
* when mapped reads are split, the alignment cigars are chopped appropriately
and the alignment start positions are adjusted (for the right end) to correctly
specify the alignment of the selected part of the read
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1402 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-10 20:42:49 +00:00
36312ae4b2
tiny cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1401 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-10 20:26:52 +00:00
921d4f4e95
RemapAlignments is a standalone picard-level tool that does not use gatk engine; moved to 'tools'
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1396 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-10 15:41:07 +00:00
089dab00e2
Was discordance rate, now concordance rate
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1393 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-07 19:37:52 +00:00
6d3ef73868
Now includes statistics on the allele agreement with dbSNP -- counts concordant calls as dbSNP = A/C and we say A/C, vs. we say A/T
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1392 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-07 19:37:07 +00:00
a864c2f025
Updated polarized reference priors, need DiploidGenotypePriors class that is directly used by the NewHotness genotypelikelihoods, more bug fixes and refactoring, etc.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1390 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-07 19:00:06 +00:00
db250f8d3e
Don't print if not in learning mode
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1389 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-07 06:08:02 +00:00
4c1fa52ddf
-Added mapping quality zero filter
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-Set some reasonable defaults (based on pilot2)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1388 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-07 03:18:02 +00:00
d60d5aa516
Fixed bug: previously reset likelihoods after each region/exon.
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Better comments/documentation added
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1386 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-05 18:44:46 +00:00
0d47798721
made booster distance a parameter
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1385 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-05 18:29:21 +00:00
3b74b3ba74
print out ref/alt ratio, not major/minor
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1384 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-05 16:36:25 +00:00
65e9dcf5b7
Fully operational version of the new genotype likelihoods class. (1) Much cleaner interface. Now explicitly stores likelihoods, priors, and posteriors in separate arrays indexed by an enum, (2) no longer can be used to make calls, it relies on SSGGenotypeCall to order the likelihoods, calculate best to ref, etc, this is just for calculating genotype likelihoods now; (3) Now performs extensive error checking with validate() to ensure the system is behaving properly. (4) fixed incorrect treatment of N bases, which we being counted against everyone (5) likely found a stats bug in which heterozyosity was being applied incorrectly to the genotype priors
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1382 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-05 01:00:55 +00:00
68309408e4
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1378 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-04 21:23:01 +00:00
45ab212f22
Post-presentation update
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1377 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-04 21:21:12 +00:00
21d1eba502
Cleaned division of responsibilities between arguments to map function. Reference has been changed
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from an array of bases to an object (ReferenceContext), and LocusContext has been renamed to reflect
the fact that it contains contextual information only about the alignments, not the locus in general.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1376 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-04 21:01:37 +00:00
a5a7d7dab8
added "booster" metrics
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1375 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-04 20:53:45 +00:00
3a8d923785
minor output changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1374 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-04 20:12:16 +00:00
939b19e715
Committing the first version of the homopolymer filter. Removes SNPs that occur at the edges of homopolymer runs and whose nonref allele matches the repeated base in the homopolymer.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1373 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-04 14:35:51 +00:00
20ff603339
New hotness and old and Busted genotype likelihood objects are now in the code base as I work towards a bug-free SSG along with a cleaner interface to the genotype likelihood object
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1372 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-03 23:07:53 +00:00
3485397483
Reorganization of the genotyping system
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1370 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-03 20:55:31 +00:00
9f1d3aed26
-Output single filtration stats file with input from all filters
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-move out isHet test to GenotypeUtils so all can use it
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1369 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-03 20:44:21 +00:00
d840a47b11
Slight reorganization of genotype interface
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1366 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-03 19:17:15 +00:00
20986a03de
cleanup before moving files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1365 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-03 19:08:24 +00:00
e3b08f245f
Pull out RMS calculation into MathUtils for all to use
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1364 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-03 17:00:20 +00:00
e495b836d3
- added mapping quality filter
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- make the filters brainless in that they strictly have thresholds and filter based on them; require user to calculate and input these thresholds.
- update filters in preparation for migration to new output format
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1363 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-03 16:46:51 +00:00
8bc925a216
Commit on the behalf of Mark: cleaning up some old and busted code in GenotypeLikelihood and associated objects.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1361 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-31 21:18:30 +00:00
9dfee7a75c
the "-genotype" option now acts correctly as a discovery mode caller in SSG
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1359 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-31 18:31:45 +00:00
9dada95ec3
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1357 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-31 16:21:16 +00:00
678c2533ca
Removed custom output stream for file and replaced with the standard out PrintStream
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1350 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-30 22:36:42 +00:00
44673b2dce
Removed a debugging println that was accidentally checked in
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1348 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-30 22:23:27 +00:00
845488ff94
VariantEval now decides whether a variant is not confidently called using BestVsNetxBest if genotypes are being evaluated and BestVsRef if not (variant discovery only). Also, the absolute value of the BestVsRef LOD (getVariantionConfidence) is used so that confident reference calls (if the GELI has output them) will show up in the final table as reference calls rather than no calls.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1347 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-30 21:54:06 +00:00
fdc7cc555b
Removed extra column name from geliHeaderString that was mislabeling the 10 genotype likelihoods by shifting them over by onex
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1345 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-30 21:42:02 +00:00
0087234ed7
small code cleanup, a couple of little changes to SSGGenotypeCall
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1343 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-30 19:47:37 +00:00
fbc7d44bc7
don't allow users to input priors anymore; they should be using heterozygosity and having the SSG calculate priors.
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Note that nothing was changed for dnSNP/hapmap priors (not sure what we want to do with these yet - any thoughts?)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1342 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-30 19:10:33 +00:00
ebanks
asivache
sjia
depristo
kcibul
hanna
mmelgar
kiran
aaron
andrewk