bigdatagenomics avocado issues

bigdatagenomics / avocado

A Variant Caller, Distributed. Apache 2 licensed.

http://bdgenomics.org/projects/avocado/

Apache License 2.0

71 stars 42 forks source link

issues

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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