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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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Outputting homozygous reference
#213
ghost
opened
4 years ago
6
GLnexus assigns a non existant SNP
#212
ghost
closed
4 years ago
5
How to filter out unknown variants?
#211
ghost
closed
4 years ago
1
pVCF representation rework
#210
mlin
opened
4 years ago
0
Any recommended parser?
#209
ghost
closed
4 years ago
3
tech debt: htslib 1.10+ breaking ABI changes
#208
mlin
opened
4 years ago
0
an error appear when use glnexus_cli
#207
berry08
closed
4 years ago
13
out of memory for large dataset
#206
hurleyLi
closed
3 years ago
9
genotyper: never revise hom-ALT to hom-REF
#205
mlin
closed
3 years ago
1
glnexus_cli speed improvements
#204
mlin
closed
4 years ago
0
Move a few BCF helper functions into their own file
#203
xunjieli
closed
4 years ago
1
DeepVariant genotyper_config::allow_partial_data
#202
mlin
closed
4 years ago
1
set unifer_config max_alleles_per_site for DeepVariant
#201
xunjieli
closed
4 years ago
3
use multi-stage Dockerfile to roll build/test & run images
#200
mlin
closed
4 years ago
1
account for discovered_alleles data structures in memory budget
#199
mlin
closed
4 years ago
2
Dockerfile multi-stage build
#198
mlin
closed
4 years ago
1
Minor change to update include path
#197
xunjieli
closed
4 years ago
1
Include alt allele trimming and full PLs to DeepVariant defaults.
#196
cmclean
closed
4 years ago
0
improve handling of DeepVariant non-called gVCF records
#195
mlin
closed
4 years ago
1
The "Performance" wiki page has moved/removed
#194
tedyun
closed
4 years ago
2
add option to trim uncalled alleles
#193
mlin
closed
4 years ago
1
RocksDB build issues with gcc 9
#192
mlin
closed
4 years ago
1
option to bcf_trim_alleles after regenotyping
#191
mlin
closed
4 years ago
0
DeepVariant preset config (v1) for WGS and WES
#190
tedyun
closed
4 years ago
2
Avoid using non-const function params in a few places
#189
xunjieli
closed
4 years ago
5
Use const std::shared_ptr<const bcf_hdr_t>& in BCFData::dataset_range
#188
xunjieli
closed
4 years ago
2
Number=R for AD
#187
brentp
closed
4 years ago
1
remove const from BCFData::dataset_header
#186
xunjieli
closed
4 years ago
1
Remove const qualifier on BCFData::dataset_header
#185
xunjieli
closed
4 years ago
3
build minimal glnexus_cli docker image in CI
#184
mlin
closed
4 years ago
1
create truly static binary with alpine+musl
#183
brentp
closed
4 years ago
3
error in make step
#182
berry08
closed
4 years ago
5
Dockerfile: use source tree in build context instead of cloning from GitHub
#181
mlin
closed
4 years ago
1
propagate PL values from reference bands
#180
mlin
closed
4 years ago
2
Move bcf_unpack before bcf1_t.d invocation
#179
xunjieli
closed
4 years ago
5
Truncated bcf file
#178
chrisfleisch
closed
4 years ago
2
docker image
#177
brentp
closed
4 years ago
7
nondeterministic sorting of "usable half-calls"
#176
mlin
closed
4 years ago
0
glnexus_cli should have -o to write out a file instead of stdout
#175
aardes
opened
5 years ago
1
refactor ingestion exceptions
#174
mlin
closed
5 years ago
1
Missing PL fields for 0/0 calls
#173
xunjieli
closed
4 years ago
12
Ability to specify a user provided configuration yaml file or ability to change presets
#172
xunjieli
closed
5 years ago
2
Performance issue with std::set used as a range filter when exome bed targets are used
#171
xunjieli
closed
5 years ago
3
avoid double-counting alleles found in multiple exome target ranges (#168)
#170
mlin
closed
5 years ago
0
install failure, how can I solve this problem?
#169
scotty323
closed
4 years ago
6
Bug in AF calculation when exome capture is used as --bed
#168
xunjieli
closed
5 years ago
4
Use min_AQ1 correctly when min_AQ2=0
#167
mlin
closed
5 years ago
2
investigate benefits of cgranges
#166
mlin
closed
5 years ago
0
min_AQ1 has no effect when min_AQ2 is zero
#165
tedyun
closed
5 years ago
3
Bug Fix - min_AQ1 is ignored when min_AQ2 is set to zero
#164
tedyun
closed
5 years ago
8
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