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Pull requests: broadinstitute/gatk

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Pull requests list

Removed restriction that physical phasing may only be run in ERC modes.
#5772 opened Mar 7, 2019 by tfenne Loading…
@tfenne
13
Updates to gatk launch script to fix properties and config file definitions. CLI
#4653 opened Apr 12, 2018 by jonn-smith Loading…
@jamesemery
4
BQSR: restore ability to specify custom covariates and to disable standard covariates
#4688 opened Apr 20, 2018 by droazen Loading… Engine-Q12019
@droazen
7
Engine read caching.
#4902 opened Jun 15, 2018 by cmnbroad Loading… Engine-Q12019
@droazen
6
Add test for index query on CRAM from Path.
#4916 opened Jun 20, 2018 by cmnbroad Loading…
@droazen
7
Adding in a config file for Funcotator.
#4960 opened Jun 27, 2018 by jonn-smith Loading…
@LeeTL1220
8
Memory-less HMM transition matrix for baseline copy-number states and silent CNV classes Copy Number tools Germline CNV
#4988 opened Jul 6, 2018 by mbabadi Loading…
@asmirnov239 @mbabadi
11
Add Python package version check to StreamingScriptExecutor.
#5081 opened Aug 2, 2018 by cmnbroad Loading… Engine-Q12019
@cmnbroad
7
cleanup up BucketUtils
#5334 opened Oct 19, 2018 by lbergelson Loading…
@droazen
5
Added the ability to reset random generation based on the start position of reads to the resivoirDownsample
#5448 opened Nov 26, 2018 by jamesemery Loading…
@droazen
8
Pulled the HaplotypeCallerIntegration tests into a common interface between spark and non-spark
#5451 opened Nov 27, 2018 by jamesemery Loading…
@droazen
8
Changed ReferenceConfidenceModel to use offsetlength counting deletions for ending comparisons bug JointCalling
#5665 opened Feb 12, 2019 by jamesemery Loading…
1
@droazen @jamesemery
10
Enable SmithWaterman AVX optimized code by default
#4356 opened Feb 6, 2018 by pnvaidya Loading…
@droazen
2
Common spark integration tests
#5723 opened Feb 26, 2019 by tomwhite Loading…
@tomwhite
3
VariantLocusWalkerSpark
#5813 opened Mar 19, 2019 by tomwhite Loading…
@tomwhite
1
Modified the gatk launch script to set MALLOC_ARENA_MAX to keep virtu…
#5849 opened Mar 31, 2019 by tfenne Loading…
@droazen
2
Adding in default value for funcotator transcript selection list.
#5872 opened Apr 9, 2019 by jonn-smith Loading…
1
@jonn-smith
13
Evoquer: a BigQuery-based joint calling tool
#6011 opened Jun 19, 2019 by droazen Loading…
@droazen
2
implement heuristics that align haplotypes to reads without calling Smith-Waterman
#6015 opened Jun 21, 2019 by jonathoncohen98 Loading…
@jonathoncohen98
70
Decoupled GCContent and reference funcotations from GencodeFuncotations Funcotator
#6033 opened Jul 12, 2019 by michaelgatzen Loading…
@jonn-smith
2
Added a new flag to ReadWalkers for start position interval filtering
#6054 opened Jul 23, 2019 by jonn-smith Loading…
@droazen
3
merged two ploidy models together and got rid of interface coding
#6082 opened Aug 7, 2019 by yonahgreene Loading…
@davidbenjamin
10
Fix 'PrintVariantsSpark crashes with serialization issues' (#3840)
#6146 opened Sep 9, 2019 by tomwhite Loading…
@lbergelson
2
Fixing an issue in the indexing of locatable XSVs and adding test. HTSJDK PRIORITY_HIGH
#6224 opened Oct 22, 2019 by jonn-smith Loading…
@jonn-smith
2
VS-1417 address ad issue in extracted vc fs
#8899 opened Jun 28, 2024 by gbggrant • Draft
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