11e85f1969
Four-base mode now estimates the genotype using the one-base method and retests the site if the one-base method suggests the site is a het.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@503 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 17:23:24 +00:00
bd719f9c06
When checking that values are not infinite, also prints out the position so that I know which site was giving the error and I can just go there and debug it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@502 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 17:21:58 +00:00
efba30f1a1
Added a constructor in which the lod threshold can be set.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@501 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 17:20:48 +00:00
8c1905c7d9
Simple walker to print all of the sample names present in a merged bam file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@500 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 12:26:56 +00:00
a3a1c9dae8
Suppressed emission of duplicate paths through a four-base pileup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@498 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 21:08:45 +00:00
6cef8bd76c
added k-best quality path enumeration.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@497 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 20:26:51 +00:00
d99d67d51c
Refactored to clean it up a bit
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@495 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 19:18:46 +00:00
ffcd672c1c
Intermediate commit while working on getting four-base probs to work in the single sample genotyper. Has infrastructure for the new combinatorial approach and just choosing the best base more intelligently given a probability distribution over bases and the reference base.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@492 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 18:06:50 +00:00
5f37ba8f26
now can be asked to log at INFO level all concordant or discordant sites, or both
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@480 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 21:03:44 +00:00
1f84b9647d
auxiliary data structure for mendelian concordance reporting; it's nice to have the latest version checked in in order for the code to compile...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@479 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 21:02:40 +00:00
ece3e9969e
one trivial walker to filter reads; bam in -> filter -> bam out
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@478 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 20:39:29 +00:00
61e855200d
latest version...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@477 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 20:38:37 +00:00
64b2fd866f
* extracted core quality-score based genotype likelihood code
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* precompute expensive operations (log/pow) based on Picard experience
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@476 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 18:58:43 +00:00
11c520b283
completed my old draft of the old school single sample genotype walker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@475 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 05:38:04 +00:00
b8233d92c8
Simple IO walker to test / crush file systems and evalute I/O performance in general
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@474 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-20 14:07:14 +00:00
bf76eab955
whoops; fix a comment line.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@473 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-19 17:54:54 +00:00
bcba1ff424
Fix a minor rounding bug and putz around with fractional counts in the pooled caller.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@472 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-19 17:52:24 +00:00
af6788fa3d
Misc:
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1. Added logGamma function to utils
2. Required asserts to be enabled in the allele caller (run with java -ea)
3. put checks and asserts of NaN and Infinity in AlleleFrequencyEstimate
4. Added option FRACTIONAL_COUNTS to the pooled caller (not working right yet)
AlleleFrequencyWalker:
5. Made FORCE_1BASE_PROBS not static in AlleleFrequencyWalker (an argument should never be static! Jeez.)
6. changed quality_precision to be 1e-4 (Q40)
7. don't adjust by quality_precision unless the qual is actually zero.
8. added more asserts for NaN and Infinity
9. put in a correction for zero probs in P_D_q
10. changed pG to be hardy-weinberg in the presence of an allele frequency prior (duh)
11. rewrote binomialProb() to not overflow on deep coverage
12. rewrote nchoosek() to behave right on deep coverage
13. put in some binomailProb() tests in the main() routine (they come out right when compared with R)
Hunt for loci where 4bp should change things:
14. added FindNonrandomSecondBestBasePiles walker.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@471 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-19 15:35:07 +00:00
758db73b98
Fixed SLOWNESS issue.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@469 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 20:10:34 +00:00
2a937fa8d3
set SAM file header's sorting order to unsorted, hopefully it will help to speed things up
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@468 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 19:32:24 +00:00
03ec3452f2
a first, simplest version of a walker that filters out reads based on user-specified criteria and writes remaining reads into a new bam file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@467 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 18:51:39 +00:00
55537c0d1e
chnage class name, now it compiles...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@451 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 16:51:00 +00:00
4f9bc7206f
some cleanup, also ensuring that all reads get written into output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@450 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 16:49:25 +00:00
e8a6cdb386
renamed standalone main
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@449 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 15:56:46 +00:00
832afd3d60
renamed standalone main
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@448 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 15:56:27 +00:00
85308f4ddc
resurrected indel tool's standalone main
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@447 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 15:55:52 +00:00
6f56938d42
* added a bit more debugging output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@446 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 15:20:26 +00:00
240eb18564
fix a few related issues when not all the reads were written into the output files. now cleaned output still contains all reads either with modified alignments or untouched
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@444 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 03:56:47 +00:00
7e05b43f40
* added some error checking for read groups
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@442 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 03:22:49 +00:00
3fda8613c3
* minor formatting changes
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* support for "extended" output
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@428 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 15:11:05 +00:00
7949e377e4
Intermediate commit. Refactored some simple base manipulation stuff into BaseUtils.java. Generalized some likelihood computation logic to make future possible EM-ing easier.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@424 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 04:18:07 +00:00
d0b8d311e6
Can now optionally print the read and the alignment region of the reference.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@423 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 04:10:30 +00:00
d4aaa1bef4
* fixed (with Matt's help) the argument parsing
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* outputting UCSC wiggle format
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@422 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 02:17:39 +00:00
24722a442e
Slight code cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@421 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 22:21:36 +00:00
baae98c6d5
and don't allocate new 200M string every time please, just pass byte array!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@417 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 21:55:33 +00:00
9d56355abe
bug fixed when reference name was passed as a string instead of actual reference bases
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@416 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 21:46:27 +00:00
222c4e5865
Commented out some debugging lines
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@415 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 20:15:41 +00:00
49d76014d1
Commented out a debugging line
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@414 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 20:15:11 +00:00
b39e584787
Primary or secondary bases that got a quality score of literally zero led to unfortunate infinities. Added an epsilon (1e-5) to every prob.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@413 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 20:04:49 +00:00
d28e9f9b98
search over q's for finding argmax[q] p(D|q)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@412 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 19:15:45 +00:00
647827b18c
Transitioned indel code to use GATK and Walkers
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@410 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 19:14:15 +00:00
961dbbd4ef
Now output bases and qhat and qstar into the GFF.
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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.
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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
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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.
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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...
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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!
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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.
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AlleleFrequencyWalker and related classes work equally well for 2 or 200 chromosomes.
Single Sample Calling:
Allele Frequency Metrics (LOD >= 5)
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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%
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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
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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.
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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
kiran
jmaguire
ebanks
asivache
kcibul
depristo