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dnanexus-rnd
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GLnexus
Scalable gVCF merging and joint variant calling for population sequencing projects
Apache License 2.0
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Trio pipeline
#163
kokyriakidis
opened
5 years ago
7
Dragen JgVCF merging
#162
MatthiasWielscher
opened
5 years ago
12
AF calculation from DeepVariant
#161
bopohdr
opened
5 years ago
7
idea: cache the last-seen reference record
#160
mlin
opened
5 years ago
0
QC of variant genotypes
#159
bopohdr
closed
5 years ago
3
Implementing BCFData directly instead of relying on RocksDB
#158
xunjieli
closed
5 years ago
3
Hotfix for handling GATK "star" alleles
#157
mlin
closed
5 years ago
0
gVCF reference depth FORMAT field is missing or malformed
#156
hurleyLi
closed
5 years ago
3
Option to create one file per region specified in regions file
#155
Alexander-Stuckey
opened
5 years ago
1
De Novo Mutation QC / Filtering
#154
dantaki
opened
5 years ago
7
Using GLnexus to merge gVCFs produced by isaac/starling
#153
Alexander-Stuckey
opened
5 years ago
2
Resume GLNexus for an existing GLnexus.DB database
#152
raonyguimaraes
opened
5 years ago
5
VQSR
#151
raonyguimaraes
opened
5 years ago
1
--bed ranges and gvcf merging
#150
HagenC
closed
4 years ago
4
travis build doesn't work on pull requests
#149
mlin
closed
4 years ago
1
parallelize allele unifier across chromosomes
#148
mlin
closed
4 years ago
3
Question on use of SyncWAL during bulk load.
#147
xunjieli
closed
5 years ago
4
Sentieon GVCFs
#146
raonyguimaraes
closed
5 years ago
3
Genotyping GVCFs from other vendors
#145
raonyguimaraes
opened
5 years ago
1
check symbolic allele without std::regex_match
#144
xunjieli
closed
5 years ago
2
FILTER (FT) liftover for Strelka2
#143
mlin
closed
5 years ago
0
Flag for using different directory path/name for "GLnexus.DB"
#142
tedyun
closed
4 years ago
1
capnproto 0.7.0
#141
mlin
closed
5 years ago
0
Add experimental Strelka2 support
#140
mlin
closed
5 years ago
0
Two DeepVariant corner cases
#139
mlin
closed
5 years ago
0
xAtlas calibration
#138
mlin
closed
6 years ago
0
Improve DP liftover field fidelity
#137
mlin
closed
6 years ago
0
QC squeezing
#136
mlin
closed
6 years ago
0
Revamp Travis builds to use docker
#135
mlin
closed
6 years ago
0
command-line options for memory and thread budgets
#134
mlin
closed
6 years ago
2
Please add a command line option to specify the number of threads GLnexus is using
#133
samfux84
closed
6 years ago
1
clean up capnp serialization in standalone mode
#132
mlin
closed
6 years ago
0
Add allele INFO fields to pVCF
#131
mlin
closed
6 years ago
1
genotyper can fill out a pVCF FORMAT field from a gVCF INFO field
#130
mlin
closed
6 years ago
1
genotyper: permit diploid calls from two overlapping gVCF variant records
#129
mlin
closed
6 years ago
1
Unify some non-left-aligned indels
#128
mlin
closed
6 years ago
1
CLI: enable loading configuration from YAML file
#127
mlin
closed
6 years ago
1
DeepVariant PL liftover
#126
mlin
closed
6 years ago
1
Update README.md
#125
mlin
closed
6 years ago
0
PoC DeepVariant gVCF merging
#124
mlin
closed
6 years ago
0
genotyper: revise low-quality homozygous calls of rare alleles
#123
mlin
closed
6 years ago
1
BCFKeyValueData skip index
#122
mlin
closed
6 years ago
4
Track the discovery target range in which alleles are found
#121
mlin
closed
6 years ago
3
BCFKeyValueData: buffer DB inserts to reduce write lock contention during bulk loads
#120
mlin
closed
6 years ago
2
Adjustments for xAtlas indels
#119
mlin
closed
6 years ago
1
weCall ingestion
#118
mlin
closed
6 years ago
1
xAtlas SNP GVCF ingestion
#117
mlin
closed
6 years ago
0
WDL workflow preparation
#116
orodeh
closed
6 years ago
1
misc efficiency improvements
#115
mlin
closed
7 years ago
1
capnp de/serialization of unified sites
#114
mlin
closed
7 years ago
3
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