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bigdatagenomics
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avocado
A Variant Caller, Distributed. Apache 2 licensed.
http://bdgenomics.org/projects/avocado/
Apache License 2.0
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[AVOCADO] Update ADAM dependency to 0.26.0.
#307
heuermh
opened
5 years ago
3
Update ADAM dependency to 0.26.0
#306
heuermh
opened
5 years ago
0
Unable to locate file from biallelicGenotyper in jointer
#305
ggittu
opened
5 years ago
0
Fixed parameter names in method documentations.
#304
jondeaton
closed
6 years ago
6
Read group dictionary contains multiple samples with identical read group names.
#303
shukwong
opened
6 years ago
0
[AVOCADO-298] Clean up Sphinx documentation build.
#302
fnothaft
closed
6 years ago
2
[AVOCADO-291] Add more helpful error message when read groups are missing
#301
fnothaft
closed
6 years ago
2
[AVOCADO-299] Bump to ADAM 0.24.0.
#300
fnothaft
closed
6 years ago
2
Bump to ADAM 0.24.0
#299
fnothaft
closed
6 years ago
0
Set minimal Sphinx version for RTD builds
#298
fnothaft
closed
6 years ago
0
Per position allele count reporting utility ( like bam-readcount)
#297
jpdna
opened
6 years ago
5
[AVOCADO-295] Set correct index when checking quality score during variant discovery.
#296
fnothaft
opened
6 years ago
2
index on quality string maybe incorrect?
#295
jpdna
closed
6 years ago
2
[AVOCADO-293] Use Spark SQL to filter variants prior to squaring off.
#294
fnothaft
closed
6 years ago
3
Use Spark SQL fully to compute variants when joint calling
#293
fnothaft
closed
6 years ago
0
[AVOCADO-289] Reduce the amount of memory consumed by observations.
#292
fnothaft
closed
6 years ago
2
Unhelpful error message for alignment files with missing read groups
#291
heuermh
closed
6 years ago
1
distribution does not include the avocado jar files
#290
pbashyal-nmdp
opened
6 years ago
0
Transient test issue
#289
fnothaft
closed
6 years ago
0
Document gVCF variant extraction flow
#288
fnothaft
closed
6 years ago
1
[AVOCADO-285] Fix bad argument names/argument name documentation.
#287
fnothaft
closed
6 years ago
2
Write original genotype prior to joint genotyping
#286
fnothaft
opened
6 years ago
0
Clean up argument names
#285
fnothaft
closed
6 years ago
0
Command to joint call gVCF
#284
jpdna
closed
6 years ago
4
Calling with Avocado using the "hive" range partitioned data
#283
jpdna
opened
6 years ago
0
Update documentation
#282
fnothaft
closed
6 years ago
1
[AVOCADO-280] Bump to ADAM 0.23.0 release.
#281
fnothaft
closed
6 years ago
2
Bump to ADAM 0.23.0 release
#280
fnothaft
closed
6 years ago
0
Variant Calling+Variant Filtering+ Variant Annotation
#279
Rokshan2016
opened
6 years ago
0
Adding code of contact adapted from the Contributor Convenant, version 1.4.
#278
heuermh
closed
6 years ago
4
Output/Single Parquet File/
#277
Rokshan2016
opened
6 years ago
0
Support banded reference model
#276
fnothaft
opened
6 years ago
0
[AVOCADO-274] Add flag to emit all genotyped variants, regardless of quality.
#275
fnothaft
opened
6 years ago
1
BiallelicGenotyper needs to be able to skip filtration
#274
fnothaft
opened
6 years ago
0
[AVOCADO-272] Support variable copy number when genotyping.
#273
fnothaft
closed
6 years ago
7
Support variable copy number when genotyping
#272
fnothaft
closed
6 years ago
0
Benchmark against Precision FDA or other "truth-sets"
#271
jpdna
opened
6 years ago
1
[AVOCADO-269] Add thresholds to DiscoverVariant CLI.
#270
fnothaft
closed
6 years ago
3
DiscoverVariants CLI doesn't support same options as BiallelicGenotyper
#269
fnothaft
closed
6 years ago
0
[AVOCADO-267] Support shuffle join in biallelic genotyper.
#268
fnothaft
closed
6 years ago
1
Support shuffle region join in biallelic genotyper
#267
fnothaft
closed
6 years ago
1
[AVOCADO-253] Add joint variant caller, direct save to VCF.
#266
fnothaft
closed
6 years ago
2
[AVOCADO-264] Add CLI for merging discovered variants across multiple samples.
#265
fnothaft
closed
6 years ago
2
Add ability to merge discovered variant sets
#264
fnothaft
closed
6 years ago
0
Uncomment save in DiscoverVariants.
#263
fnothaft
closed
6 years ago
1
[AVOCADO-259] Do not specify htsjdk or Hadoop-BAM as dependencies.
#262
fnothaft
closed
6 years ago
1
Spark Version
#261
Rokshan2016
opened
6 years ago
1
Update for breaking changes from bigdatagenomics/adam#1700.
#260
fnothaft
closed
6 years ago
3
Don't specify htsjdk or Hadoop-BAM versions
#259
fnothaft
closed
6 years ago
0
[AVOCADO-257] Add ability to discard mate info for mates on filtered contigs
#258
fnothaft
closed
6 years ago
4
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