961dbbd4ef
Now output bases and qhat and qstar into the GFF.
...
Quals coming soon (four-base)
QHAT : Most likely alt allele freq (unconstrained by number of chromosomes).
QSTAR : Most likely alt allele freq (constrained by number of chromosomes).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@402 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 15:23:00 +00:00
dafdff1974
All bases are now indexed as A:0, C:1, G:2, T:3.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@401 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 14:49:43 +00:00
bc43c0eefc
there are really cases when we can not merge until we get just two pilesant now we do not crash in those cases but print a warning and just show the resulting n piles even when n>2
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@390 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 00:45:47 +00:00
f838a5e511
Changed some double comparisons of the form a == b to abs(a - b) <= precision. Now we shouldn't be passing or failing some if conditions due to floating-point precision.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@388 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 20:05:46 +00:00
d44c30154a
added MAX_READ_LENGTH - now we can ignore long reads (454?); a bad idea in general, but the performance hit is to hard to take, at least for preliminary testing runs...
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@384 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 16:53:12 +00:00
6652f13a17
more verbose gff output!
...
EVEN MORE verbosity to come!
Tremble in anticipation.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@382 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 15:21:23 +00:00
6e180ed44e
Unified caller is go.
...
AlleleFrequencyWalker and related classes work equally well for 2 or 200 chromosomes.
Single Sample Calling:
Allele Frequency Metrics (LOD >= 5)
-------------------------------------------------
Total loci : 171575
Total called with confidence : 168615 (98.27%)
Number of variants : 111 (0.07%) (1/1519)
Fraction of variant sites in dbSNP : 87.39%
-------------------------------------------------
Hapmap metrics are coming up all zero. Will fix.
Pooled Calling:
AAF r-squared after EM is 0.99.
AAF r-squared after EM for alleles < 20% (in pools of ~100-200 chromosomes) is 0.95 (0.75 before EM)
Still not using fractional genotype counts in EM. That should improve r-squared for low frequency alleles.
Chores still outstanding:
- make a real pooled caller walker (as opposed to my experiment framework).
- add fractional genotype counts to EM cycle.
- add pool metrics to the metrics class? *shrug* we don't really have truth outside of a contrived experiment...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@380 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 12:29:51 +00:00
b4136b6d6e
a few tweaks to make it more robust: ignore reads with cigars containing anything but I,D,M; don't set up contig ordering manually, rely upon reference sequence and its dictionary; don't die if a record does not have NM tag, but faal back to direct counting instead; now requires reference as a cmdline arg
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@378 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 04:49:19 +00:00
c51f51f255
Make sure we always write at least 1000 points per base in each cycle's scatterplot. Print the disagreement rate between Bustard and FourBaseRecaller.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@375 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 00:49:41 +00:00
35fc002d5d
Debugging information is now written in such a way to make it easier to import into R.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@372 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-12 19:45:33 +00:00
6ee4fe5a20
Fixed a Bustard/Firecrest file synchronization bug.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@371 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-12 19:44:07 +00:00
817278be46
If a SAMRecord is on the negative strand, reverse complement the SQ tag.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@370 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-12 19:42:24 +00:00
1d5a22cacf
Extracts a Fastq file and the SQ tags to a separate file.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@369 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-12 19:41:44 +00:00
e410c005c0
A debugging tool to ensure the SQ tag in a four-prob SAM file matches the SAMRecord strand orientation.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@368 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-12 19:40:42 +00:00
ce72932a45
* refactored GenomeLoc to use contigIndex internally for performance and fixed several calling classes
...
* added basic unit test for GenomeLoc
* fixed bug when parsing genome locations like chr1:5000 the start position was being left as maxint rather than being set to the same as the stop position.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@365 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-12 02:25:17 +00:00
2b59110dca
CombineSamAndFourProbs is better.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@358 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-10 04:19:53 +00:00
56aa98ad30
Ignore null values.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@357 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-10 04:18:20 +00:00
2ef2c9e121
Fixed an issue wherein the SQ field was only being pulled from the first read of the pileup, no matter what. Fixed an issue wherein Andrew enumerates his bases as A:0, C:1, T:2, G:3, and Kiran's QualityUtils methods enumerate bases as A:0, C:1, G:2, T:3 (we should standardize this). Fixed an issue wherein the remaining probability was being divided by 3 rather than 2 when four-base probs are enabled.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@356 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-10 04:17:53 +00:00
17b3d5b554
New ROD accessing system, including a generalized interface for binding ROD on the command line that doesn't require you to chance GenomeAnalysisTK.java
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@355 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 22:04:59 +00:00
f5cc2d8b0b
Commented out import of IlluminaParser.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@354 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 21:30:29 +00:00
c5220c0822
Four-base probs are now decoded with the relevant method in QualityUtils
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@351 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 20:52:17 +00:00
9bc763a835
A better (aka 'working') tool for combining four-base probs with an aligned sam file.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@350 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 20:51:37 +00:00
b7a2e82b46
Can optionally process raw or corrected intensities.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@349 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 20:50:11 +00:00
6cdad10dd1
Make output type identical to the bustard parser so the values can be easily swapped for one another.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@348 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 20:49:34 +00:00
d0ce56e018
Remember to take the strand flag into account when calculating error rate per cycle as a surrogate for instrument performance.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@347 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 20:48:45 +00:00
c556a97f17
Skeleton of Somatic Coverage tool
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@342 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 02:34:03 +00:00
089bf30cf4
Send things to the out file via the logger.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@339 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 21:49:03 +00:00
6db9a00a0b
SAMFileWriter doesn't appear to flush the buffer when its destructor is called. You have to call the close() method. Also, choose a random base for Ns in the forward and reverse strands so that samtools doesn't pitch a fit.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@338 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 21:48:24 +00:00
eb2f0ebd62
If the first base of a read is 'N', and the alignment cigar says every base matches, samtools calls shennanigans. Now I just output an A, but the real way to do this is to modify the cigar string accordingly.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@337 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 19:58:18 +00:00
0e7d962eca
Oops. Slight twiddle of the math here so that I'm not asking if bestBase == nextBestBase.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@336 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 19:56:54 +00:00
62ac7366ed
A quick hack to ensure that the sequence, qualities, and secondary qualities are in accordance with the strand flag.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@331 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 15:57:28 +00:00
25474ebe7e
Computes the read error rate for a bam file. Ignores reads with indels, treats low-quality and high-quality reference bases the same. Does not count ambiguous reference bases as mismatches. Optionally allows for best two bases in read to be used.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@330 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 15:56:10 +00:00
8d48bdc9ec
it walks... the version committed actually counts snps only
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@328 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 02:00:41 +00:00
62d75ced3c
nothing fancy, just a wrapper (aka struct) to pass around a bunch of counts
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@327 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 01:58:57 +00:00
202c501939
Added a sample xml marshaller / unmarshaller.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@322 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 22:28:16 +00:00
99579a1ef8
Math correction.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@310 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 02:18:13 +00:00
9be978e006
Intermediate commit (debugging info).
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@309 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 01:20:15 +00:00
5a5c6d1276
Added some debugging stuff (writes model parameters to one file per cycle).
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@304 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-06 22:00:58 +00:00
3f75fc4e83
Unfortunately, because BWA occasionally outputs crazy reads, we need
...
to make sure not to have an ArrayIndexOutOfBoundsException thrown.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@297 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-06 03:51:35 +00:00
f12d40dde8
Simplified SAMRecord construction and emission.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@296 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-05 04:48:31 +00:00
4eac3193f7
Added RefMetaDataTracker system as a replacement for the List<RefenenceOrderedData> going into walkers. This system allows you to more easily get a tracker for processing using the lookup(name, default) system. See Pileup for an example.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@292 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-03 19:54:54 +00:00
ef06924f73
JavaDocs!
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@290 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-03 19:19:17 +00:00
bef475778f
- Updated --hapmap switch to --hapmap-chip to reflect the data being chip data for an individual rather than population allele frequency data in Hapmap
...
- Corrected some bugs to get metrics logging working
- Added a switch --force_1base_probs to ignore 4-base probalities if they exist
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@287 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-03 17:32:31 +00:00
edc44807af
rod's now have names. Use getName() to access it. Next step is better interface to accessing rods
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@286 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-03 16:41:33 +00:00
5019971290
Now outputs four-base SAM record (read name prefixed with KIR) and bustard SAM record (prefixed with BUS) for easy debugging.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@285 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-03 15:48:51 +00:00
15151ac125
Corrected the use of the prior.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@284 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-03 15:47:47 +00:00
9bbce32064
Basic dbSNP and HapMap frequency aware SNP caller... still in progress
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@282 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-03 14:24:09 +00:00
f031d882c6
ByReference traversals!
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@281 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-03 13:23:18 +00:00
e3ac0cb500
- A lot of code cleaned up; separated metrics code from AlleleFrequencyMetricsWalker into AlleleMetrics and eliminated the former class. AFMW (aside from being a name so long that it warrants an acronym) can now be implemented by passing an option to AlleleFreqeuncyWalker that logs metrics to a file.
...
- AlleleMetrics and AlleleMetricrsWalker are now ready to take a list of clasess that implement the AllelicVariant interface
- Switched a genome location in AlleleFrequencyEstimate from String to GenomeLoc which makes way more sense.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@280 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-03 02:09:10 +00:00
7d889c0661
Refactored into oblivon.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@276 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 22:12:15 +00:00
jmaguire
kiran
asivache
kcibul
depristo
hanna
ebanks
andrewk