69f5f16711
Added conditional checking for median_insert_size.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6029 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-22 17:59:54 +00:00
b35df9a0f7
Removing unnecessary String.format calls
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6028 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-22 15:30:52 +00:00
b7a1beff3c
Bug fixes and rewrite of logic of several parts in SelectVariants:
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a) If we were selecting SNPs or Indels and there was one of each at the same location, only whichever one was pulled first was processed.
b) Fixed logic error when selecting Mendelian Violations: if that option was used it wasn't possible to combine with other options.
c) Fixed logic error when using -disc option: you shouldn't parse genotypes to check whether a site is present or not because a vcf can be sites-only and this is slow.
d) Made -disc option work in the same way as other options: variants are now selected from "variant" track all the time, and variants which are not in disc track are kept. Inverse logic (keep disc variants not present in "variant") is confusing and prevents users from combining with different options.
With these changes it is now possible to ask for example "Give me all indels which are Mendelian Violations, not in dbsnp and present in these samples" which was not possible before.
Integration tests covering the above are forthcoming.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6027 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-22 14:05:00 +00:00
9b54239f37
Removed nDeletions and nInsertions as independent plots -- just not useful given nIndels and insertions/deletion ratio. Fixed jitter problems with rug plots by removing the rugs entirely. Recovered, and improved, comparative features lost by removing the rug plots by getting viewports to work (trivial) so now per sample metrics and distributions are displayed on the same page!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6026 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-22 13:59:46 +00:00
a1f8aa90c0
Added an integration test showing how to use LSF C API to get LSF parameters.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6025 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-21 22:54:55 +00:00
8e149cc52f
Fixing a silly bug of mine: when a realignment target begins at position 1 of a contig, it was possible to have some reads get emitted out of order (triggering an exception in the SAMFileWriter). This is fixed by moving around some parentheses. Tim, if you are reading this: feel free to take this fix in whenever it's convenient. I.e. it's not critical as the only user who has been hit by it has a reference with over 130K short contigs. Committing in SVN so that it gets incorporated immediately (and I can respond on GS now).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6024 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-21 21:42:38 +00:00
6dd41c8489
Nway writer takes another argument: whether to create index on the fly. Realigner in NWayOut mode currently will ALWAYS create index on the fly as there seems to be no clean way to extract the requested value from argument collection in the presence of a different @Output stream.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6023 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-21 17:26:04 +00:00
78461bac1e
Default logic (and name) has changed. Now somatic mode is default one. In order to run in single-sample (unpaired) mode, one has to use (hidden) --unpaired option.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6022 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-21 17:08:41 +00:00
c5de06a641
Fixing up the RefSeqCodec so a bad entry in RefSeq (some transcripts are odd and have a negative length which may signify something special (?) ) doesn't cause failure, but issues a warning instead. Integration tests pass.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6021 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-21 14:07:58 +00:00
7c322780d3
Nway out fixed: in this mode a special nwayout sam writer is instantiated and passed to constrained manager. All the dispatching of the reads into separate output sam streams is taken care by that writer, so no other special processing is needed at the realigner/manager level.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6020 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-20 19:35:26 +00:00
600a6a43a6
Reverting previous commit, as promised.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6019 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-20 16:30:19 +00:00
ee18c9b0c2
Temporary commit to please those in 320: re-support the -knownsOnly argument (@Hidden). This will be reverted in a sec.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6018 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-20 16:28:58 +00:00
a37e9bdbd4
Now produces an expanded table at the start, as well
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6017 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-20 13:45:08 +00:00
e8738f95c5
This warning message scares too many people.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6016 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-20 13:43:16 +00:00
4c6d0e6143
Added stratification by discrete allele count, just like AF, but requiring genotypes so it can be exact. Added docs on wiki, and integrationtest using Kiran's very nice fundamental VCF
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VariantEvalWalker now passes a pointer to itself to the Stratefication setVariantEvalWalker (and assoc. get method) so that stratefications can look at VEWalker variables to obtain information necessary for their calculations, like the list of eval samples. This is a better interface, in my opinion, than the current approach of extending the base abstract Stratefication to include an initialize function that has all arguments necessarily for any Strat.
JEXL expressions now provide access to the VariantContext vc object itself, so you can write JEXL's that directly use VariantContext and associated functions from the command line.
ExomePostQC Queue script now creates a byAC eval using the new strat, and no longer produces a byAF file (as this was not exact, and lead to strange punctile behavior when actual AF quantization was out of sync with fix quantization of AF strat.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6015 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-19 03:11:00 +00:00
907018768c
Now uses AC directly from eval, not via AF, internally for AC vs. X plotting. Requires at least 1 SNP to include a site in TiTv plotting or snp/indel ratio. Uses .byAC not .byAF eval file now
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6014 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-19 03:05:17 +00:00
64196b6c7a
Writer implementation that can dispatch reads to maltiple underlying bam files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6013 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-17 20:44:17 +00:00
1afd24c831
SliceBams now handles properly the case where multiple read groups clash in the input BAM files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6012 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-17 20:19:19 +00:00
03a0185566
Control unscattered output file location
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6011 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-17 15:53:25 +00:00
285da580f3
Now with dbSNP rate
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6010 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-17 13:21:40 +00:00
dd1d9cd76f
Forgot to deprecate the old args
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6009 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-16 17:54:44 +00:00
4e85416af1
[Foiled yet again when trying to do this in git] Slight modifications in the argument structure for the IndelRealigner. Instead of boolean flags -knownsOnly and -doNotUseSW, we now have an enum --consensusDeterminationModel which lets you specify knowns only, also use indels in reads, or also use SW. Please note that the default behavior of IR has not changed at all (and won't for a few more days) - that'll be done in GIT (fingers crossed).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6008 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-16 17:35:37 +00:00
4304fc4862
Fixed up md5s
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6007 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-16 16:20:41 +00:00
27d4b317fc
Simple program that calls indels in CEU trio exomes and WGS can compared the results. Overall the indel calls really look good to me, given reasonably good input BAM files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6006 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-16 12:56:04 +00:00
43fdd31e20
Significant performance optimization for reduced reads due to better algorithm for including reads in the variable regions. Fixed a critical bug that actually produced multiple copies of the same read in the variable regions with this optimization as well. Scala exploration script updated as well.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6005 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-16 12:54:59 +00:00
38d7733989
Now accepts any number of VCFs to evaluate. Runs the standard (now three) variant eval commands and invokes the exomeQC R script. Has some annoying assumptions about paths encoded right now. Example usage below:
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setenv DATA ~/Desktop/broadLocal/localData/
java -Djava.io.tmpdir=tmp -jar ../dist/Queue.jar -S ../scala/qscript/oneoffs/depristo/ExomePostQCEval.scala --gatkjarfile ../dist/GenomeAnalysisTK.jar -R $DATA/human_g1k_v37.fasta $* -eval $DATA/ESPGO_Gabriel_NHLBI_eomi_june_2011_batch1.vcf -intervals ~/Desktop/broadLocal/localData/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list -dbSNP ~/Desktop/broadLocal/localData/dbsnp_132_b37.vcf -eval $DATA/ESPGO_Gabriel_NHLBI_eomi_june_2011_batch2.vcf
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6004 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-16 12:49:54 +00:00
9254faa27e
Added density plots by sample for each metric. New command line argument ordering. No longer requires the per-sample.tsv suppl. data -- will conditionally load if available
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6003 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-16 12:46:29 +00:00
b4c30bf124
Added option of minMappingQuality
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6002 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-16 00:02:26 +00:00
ce4e8d2093
A few comments / todos.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6001 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-15 13:09:09 +00:00
d7430c23f8
Bringing VQSR up to date with the 1000G v2b changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6000 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-14 20:23:43 +00:00
04ecbf10ab
Fixes the constraint-generated error about stop being less than start in GenomeLocParser.createGenomeLoc.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5999 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-14 17:44:11 +00:00
14d7ee073b
Rev Picard to get new PF_INDEL_RATE metric. Rev preQC generator script
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to incorporate PF_INDEL_RATE.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5998 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-14 17:43:43 +00:00
5be4f31515
Surprisingly, the TileCovariate was indeed covered in integration tests. Updated.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5997 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-14 17:40:23 +00:00
6f7c4d1142
Removing exomePostQC.R
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5996 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-14 16:10:34 +00:00
7aec71f0e1
Add some very simple documentation on running and modifying the per-sample
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metrics generator.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5995 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-14 15:22:17 +00:00
cde2b409a7
Oops. Failed to add DbSnpMatchMetrics to Picard private jar.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5994 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-14 15:14:19 +00:00
d00d4fd4d6
Obsolete covariate class
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5993 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-14 14:11:47 +00:00
11eb74e44f
Request from Kiran: include PCT_TARGET_BASES_2X,PCT_TARGET_BASES_10X,
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PCT_TARGET_BASES_20X,PCT_TARGET_BASES_30X into pre-QC metrics.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5992 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-14 01:12:17 +00:00
1fec811a47
Updated input to accept BAM list, and output to emit proper sample name.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5991 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-14 00:15:01 +00:00
1b1aefc385
Move fingerprinting metrics reader into our Picard private extract.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5990 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-14 00:13:10 +00:00
85e20be7b7
Renamed. More general
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5989 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-13 20:50:56 +00:00
a837a49328
Minor fixes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5988 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-13 20:50:34 +00:00
e0ed30681e
If data is not available, use R-compatible 'NA' string.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5987 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-13 18:53:38 +00:00
db43e3f1ab
Fixing an apparent parenthesis matching problem
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5986 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-13 18:52:14 +00:00
52f930d708
Bug fix.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5985 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-13 18:48:55 +00:00
1d1c9da783
First pass at a script that generates per-sample metrics from a pipeline yaml
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input file. Output is an R-parseable tsv.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5984 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-13 18:38:21 +00:00
44a29680bf
Explicitly marked the updated tribble jar added in r5982 as binary
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(Oh yes, there was a r5982, in case you were wondering. It was the first
tentative git -> svn commit, and just added an updated tribble jar. It went great except for the fact that svn didn't mark the jar as binary, causing a textual diff for 500k of binary data to be generated in the notification email, cause Gsa_svn_list to very probably choke on the notification email rather than deliver it. Now let us never speak of r5982 again...)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5983 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-13 18:37:48 +00:00
480598842c
Updated the tribble jar
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5982 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-13 18:00:09 +00:00
14a358e5e8
Oops, forgot one tiny thing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5981 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-13 17:12:42 +00:00
165befd38a
V1 of the post processing QC plotting scala script and R function. The scala script runs VariantEval on a VCF file, and computes QC metrics. The R script generates the report. Will discuss usage with data processing group. Ryan -- please add your additional plotting routines to this script, as you see fit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5980 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-13 17:06:42 +00:00
kshakir
ebanks
delangel
depristo
asivache
chartl
rpoplin
fromer
hanna
droazen