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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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Add ability to discard made info for mates mapped to filtered contigs
#257
fnothaft
closed
7 years ago
0
[AVOCADO-254] Open PrefilterReads up for external use.
#256
fnothaft
closed
7 years ago
5
[AVOCADO-252] Move to ADAM 0.23.0.
#255
fnothaft
closed
7 years ago
2
Open up PrefilterReads for use externally
#254
fnothaft
closed
7 years ago
0
Add ability to save VCF directly from output of avocado
#253
fnothaft
closed
6 years ago
1
Upgrade to ADAM 0.23.0
#252
fnothaft
closed
7 years ago
0
BUILD FAILURE
#251
shibuvp
opened
7 years ago
28
[AVOCADO-249] Support BP resolution gVCF output.
#250
fnothaft
closed
6 years ago
3
Add gVCF output
#249
fnothaft
closed
6 years ago
0
Clean up INDEL allele check and filter nits for handling het alts
#248
fnothaft
closed
7 years ago
6
Don't apply HETMAXAF filter to hetalt calls
#247
fnothaft
closed
7 years ago
0
Filter out HOM other alt calls
#246
fnothaft
closed
7 years ago
0
First base of INDEL sequence is not checked
#245
fnothaft
closed
7 years ago
0
[AVOCADO-243] Score unknown alleles separately from other-alts.
#244
fnothaft
closed
7 years ago
2
Don't score as OtherAlt if read doesn't match another variant at a site
#243
fnothaft
closed
7 years ago
0
[AVOCADO-241] Don't underflow on qual 0/mapq 0 bases.
#242
fnothaft
closed
7 years ago
4
Log likelihoods underflow when qual = 0
#241
fnothaft
closed
7 years ago
0
[AVOCADO-230] Extend biallelic model to multiallelic sites.
#240
fnothaft
closed
7 years ago
2
Move genotyping unit over to Spark SQL
#239
fnothaft
closed
7 years ago
6
[AVOCADO-235] Add trio caller.
#238
fnothaft
closed
7 years ago
10
[AVOCADO-236] Rename artifacts in POM dependencies.
#237
fnothaft
closed
7 years ago
2
Update artifact names in POMs
#236
fnothaft
closed
7 years ago
0
Add trio caller
#235
fnothaft
closed
7 years ago
0
[AVOCADO-232] Make move_to_* scripts rename artifacts.
#234
fnothaft
closed
7 years ago
3
Move aggregations to Spark SQL
#233
fnothaft
closed
7 years ago
0
"Move to" scripts aren't renaming artifacts
#232
fnothaft
closed
7 years ago
0
DiscoverVariants runtime has big difference between repeated run with the same args.
#231
xubo245
opened
7 years ago
4
Clean up heterozygous alt calls
#230
fnothaft
closed
7 years ago
0
[AVOCADO-222] Add code to process high allelic fraction het calls.
#229
fnothaft
closed
7 years ago
7
[AVOCADO-226] Upgrade to ADAM 0.22.0
#228
fnothaft
closed
7 years ago
2
INDEL Allelic Fraction filters get applied to a very small number of SNPs
#227
fnothaft
closed
7 years ago
0
Move to ADAM 0.22.0
#226
fnothaft
closed
7 years ago
0
Args4j version discrepency
#225
devin-petersohn
opened
7 years ago
0
[AVOCADO-223] Fix incorrect wiring in max*AlleleFraction filters.
#224
fnothaft
closed
7 years ago
2
Misconnected max*AllelicFraction
#223
fnothaft
closed
7 years ago
0
Support relabeling high AF het calls as hom calls
#222
fnothaft
closed
7 years ago
0
[AVOCADO-220] Add allelic fraction hard filter.
#221
fnothaft
closed
7 years ago
2
Add allelic depth hard filter
#220
fnothaft
closed
7 years ago
0
[AVOCADO-218] Remove incremental compile mode.
#219
fnothaft
closed
7 years ago
2
Disable incremental build
#218
fnothaft
closed
7 years ago
0
Clean up util package
#217
fnothaft
closed
7 years ago
3
Add test coverage for CLI
#216
fnothaft
opened
7 years ago
0
Improve unittest coverage for LogPhred
#215
fnothaft
closed
7 years ago
0
Remove unused and untested files
#214
fnothaft
closed
7 years ago
0
Adding coveralls badge to README.md.
#213
fnothaft
closed
7 years ago
2
[AVOCADO-211] Push coverage reports to Coveralls.
#212
fnothaft
closed
7 years ago
8
Use Coveralls to interpret coverage reports from CI
#211
fnothaft
closed
7 years ago
0
[AVOCADO-209] Pull AvocadoKryoRegistrator back in.
#210
fnothaft
closed
7 years ago
4
Kryo NegativeArraySizeException during Forest serialization
#209
fnothaft
closed
7 years ago
0
Pass assembly variants to realigner as knowns
#208
fnothaft
opened
7 years ago
3
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