<commit_before>## 1.0.0 (in progress)

- Get from GEO server, GSM FASTQ samples using bcbio_prepare_samples.py script
- Add seqcluster stats to QC folder
- Default to no calling if `variantcaller` not specified, instead of old GATK
  UnifiedGenotyper default.
- Fix handling of fresh installs with GATK 3.6 only included. Correctly handles
  versioning from bioconda and lack of specifically defined jar directory.
- Unset JAVA_HOME when running gatk-framework and GATK > 3.6, forcing
  use of bcbio installed Java 8. Thanks to <NAME>.
- Fix bug when running realignment without recalibration in GATK 3.6. Thanks to <NAME>.
- Allow PED based gender specifications (1=male, 2=female). Thanks to <NAME>.
- Allow non-positional UMI Rapmap quantified single-cell RNA-seq.
- Re-enable save_diskspace option to reduce disk usage during alignment
  preparation and split alignments.
- Offload fixing the unmapped Tophat file to tophat-recondition. Thanks to <NAME>.
- Add support for vcfanno (https://github.com/brentp/vcfanno) to annotate VCFs with other 
  VCFs/BED files. 
- Mark possible RNA-edits for GRCh37/hg19 using RADAR coordinates. Thanks to <NAME>
  for the suggestion. 

## 0.9.9 (18 July 2016)

- Change defaults for recalibration and realignment to False. These have been
  the recommended settings (http://bit.ly/bcbio-minimal) and no realignment now
  matches Broad recommendations.
- Use conda installed Java instead of requiring external installation
  for most tools.
- Support GATK 3.6 with Java 8 installed as part of anaconda. Older GATK
  versions for calling and recalibration/realignment require external Java 7.
- Re-organization of variants stats using bcftools and
  cleaning gemini queries to get individual samples metrics.
- Quality control back end revamped to support better parallelization
  and pluggability of new QC metrics.
- Support CNV calling with Seq2C for exome, targeted or amplicon experiments.
  Thanks to <NAME>.
- Add `fixrg` target to `bam_clean` to accept BAM inputs with correct<commit_msg>Fix spelling of my name.<commit_after>## 1.0.0 (in progress)

- Get from GEO server, GSM FASTQ samples using bcbio_prepare_samples.py script
- Add seqcluster stats to QC folder
- Default to no calling if `variantcaller` not specified, instead of old GATK
  UnifiedGenotyper default.
- Fix handling of fresh installs with GATK 3.6 only included. Correctly handles
  versioning from bioconda and lack of specifically defined jar directory.
- Unset JAVA_HOME when running gatk-framework and GATK > 3.6, forcing
  use of bcbio installed Java 8. Thanks to <NAME>.
- Fix bug when running realignment without recalibration in GATK 3.6. Thanks to <NAME>.
- Allow PED based gender specifications (1=male, 2=female). Thanks to <NAME>.
- Allow non-positional UMI Rapmap quantified single-cell RNA-seq.
- Re-enable save_diskspace option to reduce disk usage during alignment
  preparation and split alignments.
- Offload fixing the unmapped Tophat file to tophat-recondition. Thanks to <NAME>.
- Add support for vcfanno (https://github.com/brentp/vcfanno) to annotate VCFs with other 
  VCFs/BED files. 
- Mark possible RNA-edits for GRCh37/hg19 using RADAR coordinates. Thanks to <NAME>
  for the suggestion. 

## 0.9.9 (18 July 2016)

- Change defaults for recalibration and realignment to False. These have been
  the recommended settings (http://bit.ly/bcbio-minimal) and no realignment now
  matches Broad recommendations.
- Use conda installed Java instead of requiring external installation
  for most tools.
- Support GATK 3.6 with Java 8 installed as part of anaconda. Older GATK
  versions for calling and recalibration/realignment require external Java 7.
- Re-organization of variants stats using bcftools and
  cleaning gemini queries to get individual samples metrics.
- Quality control back end revamped to support better parallelization
  and pluggability of new QC metrics.
- Support CNV calling with Seq2C for exome, targeted or amplicon experiments.
  Thanks to <NAME>.
- Add `fixrg` target to `bam_clean` to accept BAM inputs with correct
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