broadinstitute gatk-protected issues

broadinstitute / gatk-protected

Obsolete/Legacy GATK repository -- go to https://github.com/broadinstitute/gatk instead

BSD 3-Clause "New" or "Revised" License

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bed file question

#1135 milkcookie closed 6 years ago
1
Added clear deprecation notice

#1134 vdauwera closed 7 years ago
1
M2FiltersArgumentCollection arguments are not recognized by Mutect2 nor do they show up in the docs

#1133 sooheelee closed 7 years ago
5
Updated github issue numbers on gCNV TODO comments

#1132 droazen opened 7 years ago
2
Other tools: tag docs, label internal, add minimal formatting

#1131 sooheelee closed 7 years ago
1
CNV tools: archive 3 tools and related tests

#1130 sooheelee opened 7 years ago
11
CNV 3 tools: tag docs; label internal in one-line summary

#1129 sooheelee closed 7 years ago
1
CNV CollectAllelicCounts and CreateAllelicPanelOfNormals

#1128 sooheelee closed 7 years ago
1
CNV GetHetCoverage: mention tool is non-bayesian version of GetBeyesianHetCoverage

#1127 sooheelee closed 7 years ago
2
CNV GetHetCoverage: mention tool is non-bayesian version of GetBeyesianHetCoverage

#1126 sooheelee closed 7 years ago
1
CNV GetBayesianHetCoverage: tag doc, give example command and interval_list, massage summary, pri…

#1125 sooheelee closed 7 years ago
1
CNV getbayesianhetcoverage: tag doc, give example command and interval_list, massage summary, prioritize modes

#1124 sooheelee closed 7 years ago
1
CNV plotacnvresults: tag doc, give example command, detail dictionary handling

#1123 sooheelee closed 7 years ago
1
CNV PerformJointSegmentation: tag doc

#1122 sooheelee closed 7 years ago
1
CNV PerformCopyRatioSegmentation: tag doc

#1121 sooheelee closed 7 years ago
1
CNV performallelefractionsegmentation: tag doc

#1120 sooheelee closed 7 years ago
4
CNV PerformAlleleFractionSegmentation: Shl doc perform allele fraction segmentation

#1119 sooheelee closed 7 years ago
5
CNV CorrectGCBias: Shl doc correct gc bias

#1118 sooheelee closed 7 years ago
1
CNV ConvertGSVariantsToSegments: tag doc, give example command and example output

#1117 sooheelee closed 7 years ago
1
Provide mutect equations in pdf format, not just .tex laTex format

#1116 sooheelee closed 7 years ago
1
Add command line/program to generated VCFs.

#1115 cmnbroad closed 7 years ago
1
Use bigger kmers in assembly

#1114 davidbenjamin closed 7 years ago
2
Experiment with minBaseQualityScore in Mutect

#1113 davidbenjamin closed 7 years ago
1
Is it really necessary to "prepare likelihoods for annotation"?

#1112 davidbenjamin closed 7 years ago
1
Downsample ref reads in Mutect

#1111 davidbenjamin closed 7 years ago
1
Filter reads more aggressively in Mutect

#1110 davidbenjamin closed 7 years ago
1
Duplicate read filter for cell-free DNA data with UMI

#1109 takutosato closed 7 years ago
3
HaplotypeCallorSpark "ArrayIndexOutOfBoundsException"

#1108 TianJin297 closed 7 years ago
1
HaplotypeCallorSpark "Duplicate key" error

#1107 TianJin297 closed 7 years ago
1
NormalizeSomaticReadCounts has ``targets`` parameter as optional, but it is required.

#1106 LeeTL1220 closed 7 years ago
1
Change docgen field search order.

#1105 cmnbroad closed 7 years ago
1
Approx. date for merging "protected" into "public"?

#1104 magicDGS closed 7 years ago
4
Polishing M2 wdls

#1103 davidbenjamin closed 7 years ago
2
CNV TargetCoverageSexGenotyper: tag doc, give example command and add notes from MB's email

#1102 sooheelee closed 7 years ago
3
Update license and readme

#1101 vdauwera closed 7 years ago
1
Update README.md

#1100 vdauwera closed 7 years ago
0
Update LICENSE.txt

#1099 vdauwera closed 7 years ago
0
Generative model for orientation bias

#1098 davidbenjamin closed 7 years ago
1
Poisson regression is not robust to outliers and leads to wrong inferences in TargetCoverageSexGenotyper

#1097 mbabadi closed 7 years ago
1
CNV GermlineCNVCaller: tag doc, give two example commands, point to results folders

#1096 sooheelee closed 7 years ago
3
Fixing a NPE that could come up in cases of multiallelic sites.

#1095 LeeTL1220 closed 7 years ago
0
Be more discriminating about soft clips in active region determination

#1094 davidbenjamin closed 7 years ago
4
CNV PadTargets: tag doc and give example command

#1093 sooheelee closed 7 years ago
3
fix test in GenotypeGVCFsIntegrationTest

#1092 lbergelson closed 7 years ago
2
IllegalArgumentException in HaplotypeCallerSpark

#1091 tomwhite closed 7 years ago
2
Count different kinds of alt reads in M2 isActive

#1090 davidbenjamin closed 7 years ago
1
Account for base qualities in M2 isActive

#1089 davidbenjamin closed 7 years ago
1
Updated github issue numbers on gCNV TODO comments

#1088 mbabadi closed 7 years ago
2
For ConvertACNVResults documentation, descriptions and examples of ACS and TITAN

#1087 sooheelee closed 7 years ago
1
Evaluate TargetCoverageSexGenotyper on WGS samples

#1086 mbabadi closed 7 years ago
1