bigdatagenomics/avocado

Issues

• Update ADAM dependency to 0.26.0

  #306 opened 6 years ago by heuermh
  0

• Unable to locate file from biallelicGenotyper in jointer

  #305 opened 6 years ago by ggittu
  0

• Read group dictionary contains multiple samples with identical read group names.

  #303 opened 7 years ago by shukwong
  0

• Unhelpful error message for alignment files with missing read groups

  #291 opened 7 years ago by heuermh
  1

• Set minimal Sphinx version for RTD builds

  #298 opened 7 years ago by fnothaft
  0

• Bump to ADAM 0.24.0

  #299 opened 7 years ago by fnothaft
  0

• index on quality string maybe incorrect?

  #295 opened 7 years ago by jpdna
  2

• Support shuffle region join in biallelic genotyper

  #267 opened 7 years ago by fnothaft
  1

• Use Spark SQL fully to compute variants when joint calling

  #293 opened 7 years ago by fnothaft
  0

• Transient test issue

  #289 opened 7 years ago by fnothaft
  0

• Write original genotype prior to joint genotyping

  #286 opened 7 years ago by fnothaft
  0

• distribution does not include the avocado jar files

  #290 opened 7 years ago by pbashyal-nmdp
  0

• Command to joint call gVCF

  #284 opened 7 years ago by jpdna
  4

• Document gVCF variant extraction flow

  #288 opened 7 years ago by fnothaft
  1

• Clean up argument names

  #285 opened 7 years ago by fnothaft
  0

• Update documentation

  #282 opened 7 years ago by fnothaft
  1

• Calling with Avocado using the "hive" range partitioned data

  #283 opened 7 years ago by jpdna
  0

• BiallelicGenotyper needs to be able to skip filtration

  #274 opened 7 years ago by fnothaft
  0

• Support variable copy number when genotyping

  #272 opened 7 years ago by fnothaft
  0

• Bump to ADAM 0.23.0 release

  #280 opened 7 years ago by fnothaft
  0

• Variant Calling+Variant Filtering+ Variant Annotation

  #279 opened 7 years ago by Rokshan2016
  0

• Output/Single Parquet File/

  #277 opened 7 years ago by Rokshan2016
  0

• Support banded reference model

  #276 opened 7 years ago by fnothaft
  0

• Add ability to save VCF directly from output of avocado

  #253 opened 7 years ago by fnothaft
  1

• Add gVCF output

  #249 opened 7 years ago by fnothaft
  0

• Benchmark against Precision FDA or other "truth-sets"

  #271 opened 7 years ago by jpdna
  1

• DiscoverVariants CLI doesn't support same options as BiallelicGenotyper

  #269 opened 7 years ago by fnothaft
  0

• Add ability to merge discovered variant sets

  #264 opened 7 years ago by fnothaft
  0

• Don't specify htsjdk or Hadoop-BAM versions

  #259 opened 7 years ago by fnothaft
  0

• Spark Version

  #261 opened 8 years ago by Rokshan2016
  1

• Add ability to discard made info for mates mapped to filtered contigs

  #257 opened 8 years ago by fnothaft
  0

• Open up PrefilterReads for use externally

  #254 opened 8 years ago by fnothaft
  0

• Upgrade to ADAM 0.23.0

  #252 opened 8 years ago by fnothaft
  0

• BUILD FAILURE

  #251 opened 8 years ago by shibuvp
  28

• Filter out HOM other alt calls

  #246 opened 8 years ago by fnothaft
  0

• Don't apply HETMAXAF filter to hetalt calls

  #247 opened 8 years ago by fnothaft
  0

• First base of INDEL sequence is not checked

  #245 opened 8 years ago by fnothaft
  0

• INDEL Allelic Fraction filters get applied to a very small number of SNPs

  #227 opened 8 years ago by fnothaft
  0

• Support relabeling high AF het calls as hom calls

  #222 opened 8 years ago by fnothaft
  0

• Don't score as OtherAlt if read doesn't match another variant at a site

  #243 opened 8 years ago by fnothaft
  0

• Log likelihoods underflow when qual = 0

  #241 opened 8 years ago by fnothaft
  0

• Clean up heterozygous alt calls

  #230 opened 8 years ago by fnothaft
  0

• Move aggregations to Spark SQL

  #233 opened 8 years ago by fnothaft
  0

• Add trio caller

  #235 opened 8 years ago by fnothaft
  0

• Update artifact names in POMs

  #236 opened 8 years ago by fnothaft
  0

• DiscoverVariants runtime has big difference between repeated run with the same args.

  #231 opened 8 years ago by xubo245
  4

• "Move to" scripts aren't renaming artifacts

  #232 opened 8 years ago by fnothaft
  0

• Move to ADAM 0.22.0

  #226 opened 8 years ago by fnothaft
  0

• Args4j version discrepency

  #225 opened 8 years ago by devin-petersohn
  0

• Misconnected max*AllelicFraction

  #223 opened 8 years ago by fnothaft
  0