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14468 Commits (85cb1c281068e563c31e8bce00012586a40d5df9)

Author SHA1 Message Date
Samuel Friedman 85cb1c2810 dont spam on NaNs 2017-04-26 17:33:06 -04:00
Samuel Friedman 57c064eaa3 small code cleanup 2017-04-26 16:02:06 -04:00
Samuel Friedman a8f70c891f Create GMM from model reports in VQSR 2017-04-26 16:02:06 -04:00
skwalker 4fe4ace232 minor bug fix in depth of coverage for partitioning by library + test (#1574) 
minor bug fix in depth of coverage for partitioning by library
 2017-04-26 10:42:54 -04:00
droazen 5110b13124 Merge pull request #1572 from broadinstitute/dr_use_gkl_intel_inflater_deflater 
Add the Intel GKL as a dependency, and turn on the Intel inflater/deflater by default
 2017-04-14 16:22:34 -04:00
David Roazen a950d0778f Add the Intel GKL as a dependency, and turn on the Intel inflater/deflater by default 2017-04-05 12:45:26 -04:00
Ron Levine 728b3db8e0 Merge pull request #1571 from broadinstitute/rhl_vtbp_doc_1570 
Update PLINK link and change lines to columns
 2017-03-23 14:22:05 -04:00
Ron Levine 278985b8bd Update PLINK link and change lines to columns 2017-03-23 11:46:38 -04:00
Ron Levine 485a090ef6 Merge pull request #1569 from broadinstitute/rhl_vtt_doc_orders_samples_1545 
Document how VTT orders samples in output table
 2017-03-21 18:09:35 -04:00
Ron Levine 00a434a38b Merge pull request #1568 from broadinstitute/rhl_mutect2_doc_germline_1560 
Update MuTect2 documentation about not computing obvious germline variants
 2017-03-21 18:08:39 -04:00
Ron Levine 4188745074 Document how VTT orders samples in output table 2017-03-21 18:04:38 -04:00
Ron Levine c20e682a97 Update MuTect2 documentation about not computing obvious germline variants 2017-03-21 17:54:52 -04:00
Ron Levine c449b133d0 Merge pull request #1565 from broadinstitute/rhl_fix_cv_merge_1547 
Fix CombineVariants merge for different types
 2017-03-14 16:43:33 -04:00
Ron Levine 687dee22ac Fix CombineVariants merge for different types 2017-03-14 16:42:16 -04:00
Ron Levine 31315a31c0 Merge pull request #1563 from broadinstitute/rhl_fci_thresholds_1562 
Fix FindCoveredIntervals so -minBQ, -minMQ and -cov work as expected
 2017-03-07 17:07:45 -05:00
Ron Levine 49083fc704 Fix FindCoveredIntervals so -minBQ, -minMQ and -cov work as expected 2017-03-07 16:58:23 -05:00
Ron Levine b3df32047f Merge pull request #1535 from broadinstitute/rhl_clipping_op_align_offset_1447 
Fixed ClippingOP.getNewAlignmentStartOffset() to handle N cases properly
 2017-03-06 17:53:12 -05:00
Ron Levine 1e88d849e3 Fixed ClippingOP.getNewAlignmentStartOffset() to handle N cases properly and added unit test 2017-03-06 15:40:01 -05:00
Ron Levine faeac6e5a4 Merge pull request #1551 from broadinstitute/rhl_hc_no_dp_ad_1322 
Set AD and DP to zero if no read coverage
 2017-02-28 16:58:21 -05:00
Ron Levine 8316fa92f3 Set AD and DP to zero if no read coverage 2017-02-28 16:56:45 -05:00
Ron Levine c0bf07cb78 Merge pull request #1559 from broadinstitute/rhl_htsjdk_2.9.1_picard_2.9.0 
Move htsjdk to ver 2.9.1 and picard to ver 2.9.0
 2017-02-23 14:32:44 -05:00
Ron Levine 91339c12c9 Move htsjdk to ver 2.9.1 and picard to ver 2.9.0 2017-02-22 19:01:26 -05:00
Ron Levine 5c178c2a84 Merge pull request #1553 from broadinstitute/rhl_latv_split_nocall_1518 
Fix LeftAlignAndTrimVariants -split to not change no-call genotypes to hom-ref
 2017-02-22 18:54:26 -05:00
Ron Levine 61875e4dfa Fix LeftAlignAndTrimVariants -split to not change no-call genotypes to hom-ref 2017-02-22 17:57:59 -05:00
Ron Levine b9a43cc35e Merge pull request #1557 from broadinstitute/rhl_ggvcfs_input_prior_1532 
Total ploidy does not have to equal to the number of priors
 2017-02-20 22:21:25 -05:00
Ron Levine 3c347c1385 Total ploidy does not have to equal to the number of priors 2017-02-20 20:28:41 -05:00
Ron Levine c55c77ab27 Merge pull request #1555 from broadinstitute/rhl_htsjdk_2.9.0_picard_2.8.3 
Move htsjdk to ver 2.9.0 and picard to ver 2.8.3
 2017-02-17 13:54:17 -05:00
Ron Levine ab75b08ea7 Remove unused compressed_block_size and close BlockCompressedInputStream 2017-02-17 12:22:53 -05:00
Ron Levine 1d36d9fd69 Move htsjdk to ver 2.9.0 and picard to ver 2.8.3 2017-02-17 07:03:03 -05:00
Ron Levine 67baa9046c Merge pull request #1550 from broadinstitute/rhl_fix_splitncigarreads_doc_1549 
Change ALLOW_N_CIGARS to ALLOW_N_CIGAR_READS in doc
 2017-01-18 17:06:06 -05:00
Ron Levine dce2e29ade Change ALLOW_N_CIGARS to ALLOW_N_CIGAR_READS in doc 2017-01-18 15:11:52 -05:00
Ron Levine 7c0e51396f Merge pull request #1539 from broadinstitute/rhl_hc_disable_badmatefilter_1443 
Allow disabling of BadMateFilter in HaplotypeCaller
 2017-01-18 12:39:22 -05:00
Ron Levine bfa633a90f Merge pull request #1548 from broadinstitute/rhl_synchonize_upstream_del_1188 
Make upstreamDeletionsLoc Thread Safe
 2017-01-13 14:57:05 -05:00
Ron Levine 1f6645539a Make upstreamDeletionsLoc ThreadLocal 2017-01-12 14:09:24 -05:00
Ron Levine f092e1438d Allow disabling of BadMateFilter in HaplotypeCaller 2017-01-11 14:49:45 -05:00
Ron Levine bb87730ddc Merge pull request #1546 from broadinstitute/rhl_annot_warn_1540 
Log annotation warning once if using multithreads
 2017-01-09 11:59:53 -05:00
Ron Levine 44c0609418 Log annotation warning once if using multithreads 2017-01-08 09:58:40 -05:00
Ron Levine c5df90b598 Merge pull request #1544 from broadinstitute/rhl_thread_safety_1543 
Synchronize modification/access to practicalAlleleCountForPloidy
 2017-01-07 10:00:18 -05:00
Ron Levine 4f52395795 Synchronize modification/access to practicalAlleleCountForPloidy 2017-01-06 22:16:35 -05:00
Ron Levine 7447616766 Merge pull request #1542 from broadinstitute/rhl_update_stand_call_conf_doc_1538 
Update stand_call_conf doc string
 2017-01-06 20:42:56 -05:00
Ron Levine ab4a9fa64f Update stand_call_conf doc strings 2017-01-06 17:15:56 -05:00
Geraldine Van der Auwera e86da63d04 Update pom versions to mark the start of GATK 3.8 development 2016-12-12 08:53:23 -05:00
Geraldine Van der Auwera 56f2c1ac75 Update pom versions for the 3.7 release 2016-12-12 08:49:43 -05:00
Geraldine Van der Auwera 49c1a6c7bd Merge remote-tracking branch 'unstable/master' 2016-12-12 08:48:29 -05:00
Geraldine Van der Auwera dca24a9fa4 Merge pull request #1533 from broadinstitute/lb_update_jexl_behavior 
Rev htsjdk + update jexl behavior
 2016-12-10 13:33:06 -05:00
Ron Levine 5602095a24 Move htsjdk to ver 2.8.1 and picard to ver 2.7.2 
- Updating VF and tests to match new jexl behavior from htsjdk
     - Use Z instead of DP to test behavior on missing annotation
 2016-12-10 11:50:30 -05:00
meganshand 1291cfa881 Merge pull request #1529 from broadinstitute/ms_fs 
Make Fisher Exact Test match R and GATK4 p-values
 2016-12-06 08:55:08 -05:00
Ron Levine 24336e85b6 Merge pull request #1528 from broadinstitute/rhl_validate_vcf.gz 
Output filenames with the vcf.gz extension are gzipped, those containing the string ".bcf" result in VCF
 2016-12-06 06:46:15 -05:00
Ron Levine 172db666d6 Output files with the vcf.gz extension are gzipped, containing .bcf not as an extension result in VCF" 2016-12-05 22:25:59 -05:00
Geraldine Van der Auwera 234ccdf0c3 Merge pull request #1496 from broadinstitute/db_m2_downsampling 
Expose downsampling parameters as CLI arguments to Mutect2
 2016-12-05 21:53:25 -05:00