Menachem Fromer
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ce4d702e25
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No-calls and filtered genotypes are now properly considered missing
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2011-07-15 14:36:37 -04:00 |
Mauricio Carneiro
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7b7d40d5d9
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A better name for the qscript utilities. Throw here every method you find yourself repeatedly implementing in your qscripts!
Refactoring appropriately.
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2011-07-15 14:34:50 -04:00 |
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Mauricio Carneiro
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a670d6420a
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Refactoring Qscript utils into queue general utils package.
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2011-07-15 14:31:43 -04:00 |
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Menachem Fromer
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c2c8df49e1
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Can specify the phasing/child sample on the command-line.
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2011-07-15 13:46:24 -04:00 |
Kiran V Garimella
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760abf2bc9
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Merge branch 'desktop'
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2011-07-15 09:38:42 -04:00 |
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Kiran V Garimella
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f10fa3180e
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Bug fix to walker that computes missing genotype error
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2011-07-15 09:38:21 -04:00 |
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Kiran V Garimella
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c5667429a9
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Merge branch 'desktop'
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2011-07-15 09:28:17 -04:00 |
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Kiran V Garimella
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c0889df90e
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Walker to compute missing genotype error - a metric to assess the quality of imputation
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2011-07-15 09:27:04 -04:00 |
Guillermo del Angel
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9283ac906e
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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
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2011-07-14 19:16:46 -04:00 |
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Guillermo del Angel
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6620ebd8d8
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Changes to indel VQSR consensus creation script
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2011-07-14 19:16:14 -04:00 |
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Mauricio Carneiro
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f19862a643
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Fixing conflicts.
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2011-07-14 17:13:31 -04:00 |
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Mauricio Carneiro
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43c6a8565b
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looks better now.
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2011-07-14 17:10:44 -04:00 |
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Mauricio Carneiro
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09ffe277ae
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Added a qscripts util package with some utility functions commonly shared across queue scripts. Refactored some of my public scripts to use it in an effort to make queue scripts more reusable and "supportable".
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2011-07-14 17:09:35 -04:00 |
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Mauricio Carneiro
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4f8230c750
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Merged bug fix from Stable into Unstable
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2011-07-14 16:44:57 -04:00 |
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Mauricio Carneiro
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9f5180ab05
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Recalibrates a list of bam files allowing multiple bams to be recalibrated out of a single 'mother' queue job.
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2011-07-14 16:42:17 -04:00 |
Mark DePristo
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c0bbeb23ba
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Now providing more information when the index on the fly isn't equal to the one created by reading the file from disk.
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2011-07-14 15:12:28 -04:00 |
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Mark DePristo
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5ffeddd3b1
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better to use _ instead of ., as this is a special case later.
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2011-07-14 14:45:16 -04:00 |
Eric Banks
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9540df6998
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Oops, forgot to update unit test
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2011-07-14 14:00:19 -04:00 |
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Eric Banks
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ed6beae1f3
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Adding headers to diffable reading for VCFs
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2011-07-14 13:55:35 -04:00 |
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Eric Banks
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57a90173f3
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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
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2011-07-14 11:56:20 -04:00 |
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Eric Banks
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66c652d687
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Added some extra error checks in the VCF codec. Now that we've moved this back into the GATK, changed some of the standard exceptions to be USerErrors (instead of TribbleExceptions).
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2011-07-14 11:56:10 -04:00 |
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Mark DePristo
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ad373ffa7e
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Broke down and implemented parallel get. Now running 10x parallel no problems on gsa1.
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2011-07-14 09:12:43 -04:00 |
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Mark DePristo
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1390f354dc
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Giving up on parallel s3 fetching. The solution here is to do incremental processing, and not try to download 1.5M records at once, but obtain the ~10K per day that are appearing.
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2011-07-13 23:12:19 -04:00 |
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Kiran V Garimella
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af9b7f27eb
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Readded ComputeSwitchErrorRate
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2011-07-13 23:04:23 -04:00 |
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Kiran V Garimella
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db7a23d896
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Added check to only evaluate phased genotypes, in case I ever want to use this program on another file that's not guaranteed to have every genotype phased.
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2011-07-13 22:58:04 -04:00 |
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Mark DePristo
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ae044af678
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Forgot to comment out a debug
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2011-07-13 22:39:58 -04:00 |
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Mark DePristo
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caa3629467
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Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
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2011-07-13 22:38:27 -04:00 |
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Mark DePristo
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d6c1540e57
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Parallel version.
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2011-07-13 22:37:49 -04:00 |
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Mark DePristo
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63c58c5f7e
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Log file no longer optional.
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2011-07-13 21:41:15 -04:00 |
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Mark DePristo
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d163a2106a
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Now uses the log file to determine which files exist locally, avoiding the potentially expensive check on disk
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2011-07-13 21:36:02 -04:00 |
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Mauricio Carneiro
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a4ab19d040
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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
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2011-07-13 15:14:06 -04:00 |
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Eric Banks
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0c54c796ed
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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
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2011-07-13 14:57:33 -04:00 |
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Eric Banks
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bb0e3a26fc
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Added integration test for VCF writing. Also, bug fix for writing the GT-free records.
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2011-07-13 14:57:21 -04:00 |
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Mauricio Carneiro
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df996a1a73
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more progress report for the Data Processing Pipeline.
Bam lists can now have empty lines, comments and whitespaces anywhere.
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2011-07-13 14:53:58 -04:00 |
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Eric Banks
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6a431da554
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Don't output source and ref header lines anymore. Short-term motivation for this is that I'd like this tool when run on a VCF to emit the exact same VCF. Long-term motivation is that these tags should be output by the VCF writer itself for all tools.
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2011-07-13 14:40:01 -04:00 |
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Mauricio Carneiro
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e2f2917bd2
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Merged bug fix from Stable into Unstable
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2011-07-13 13:00:55 -04:00 |
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Mauricio Carneiro
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ff4e31c554
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Changing the file names as per Kris request.
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2011-07-13 12:59:18 -04:00 |
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Menachem Fromer
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74aa49e423
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Merged bug fix from Stable into Unstable
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2011-07-13 12:12:42 -04:00 |
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Menachem Fromer
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fa3ff53508
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Filters should only be applied to the new VC if the old VC had filters applied
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2011-07-13 11:58:16 -04:00 |
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Mark DePristo
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e86113e537
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Minor fixes for logging. Now logs even if you don't need to download the file (it's a complete log now).
Bug fix for del logging.
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2011-07-13 10:27:24 -04:00 |
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Mark DePristo
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b04b8b20a5
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Added support for -p log so that we can track progress without trying to ls a directory with 1.5M entries in it.
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2011-07-13 10:22:32 -04:00 |
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Mark DePristo
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6450b48951
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manageGATKS3Logs now downloads and deletes files in groups of 100 files by default. This should significantly improve the performance of the S3 log synchronization.
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2011-07-13 10:14:38 -04:00 |
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Eric Banks
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969227c657
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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
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2011-07-13 10:01:28 -04:00 |
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Eric Banks
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797c50e689
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Fixing integration tests I broke yesterday; removing batch merging test since we don't support that anymore.
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2011-07-13 10:01:23 -04:00 |
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Eric Banks
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6007eea3ff
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Allowing VCF records without GTs in vf4.1
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2011-07-13 09:56:08 -04:00 |
Christopher Hartl
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95040d95b9
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Adding in check for filtered site (Sorry Mark, looks like it wasn't checking the validated rod, only the mask). Also by allowing user to lowercase SNPs, could miss 'SNP_TOO_NEAR_PROBE', now we properly check for that.
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2011-07-12 19:21:26 -04:00 |
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Christopher Hartl
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61dad4f090
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Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
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2011-07-12 18:33:30 -04:00 |
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Christopher Hartl
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30768eccbb
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Big change to PSP2: Amplicon sequence no longer lower-cased for repetitiveness, but instead for non-uniqueness via alignment by bwa. Performance heavily dependent on length of sequence (duh), with size=30 a good balance, but default is 20 because that's the default length of a sequenom primer. Indentation changes to other stuff.
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2011-07-12 18:33:12 -04:00 |
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Mauricio Carneiro
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60870b360a
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Fixed the calculation of the allele count prior, it was using ac instead of maxAlleleCount.
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2011-07-12 17:18:52 -04:00 |
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Mauricio Carneiro
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d21388f0cb
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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
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2011-07-12 15:56:38 -04:00 |