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Allow spark tools to write bcf files #4303

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lbergelson opened this issue Jan 29, 2018 · 0 comments
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Allow spark tools to write bcf files #4303

lbergelson opened this issue Jan 29, 2018 · 0 comments
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@tomwhite
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@lbergelson
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lbergelson commented Jan 29, 2018 •
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Currently we can't write bcf files from VariantSparkSink. This may require a fix in hadoop bam.
We should also enable writing g.bcf and bcf.gz variants.
@lbergelson lbergelson changed the title Allow spark to write g.bcf files Allow spark tools to write g.bcf files Jan 29, 2018
This was referenced Jan 29, 2018
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@droazen droazen modified the milestones: Engine-4.1, Engine-1Q2018 Feb 5, 2018
@tomwhite tomwhite mentioned this issue Feb 27, 2018
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@droazen droazen modified the milestones: Engine-1Q2018, Engine-2Q2018 Apr 6, 2018
@tomwhite tomwhite mentioned this issue May 2, 2018
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@lbergelson lbergelson changed the title Allow spark tools to write g.bcf files Allow spark tools to write bcf files May 10, 2018
lbergelson pushed a commit that referenced this issue May 10, 2018
@tomwhite @lbergelson
Support g.vcf.gz files in Spark. #4274 (#4463)
5b4f861 
* Support g.vcf.gz files in Spark tools
* fixes #4274 
* upgrade hadoop-bam 7.9.1 -> 7.10.0
* Remove bcf files from Spark tests since spark currently can't write bcf files correctly 
   * this is tracked by #4303 
   * a file called named .bcf is produced, but the file is actually encoded as a vcf
   * updated tests to verify that the file extension matches the actual datatype in the file
@droazen droazen removed this from the Engine-2Q2018 milestone Oct 4, 2018
zaneChou1 added a commit to zaneChou1/gatk that referenced this issue Nov 12, 2020
@zaneChou1
Support BCF files in Spark. broadinstitute#4303
765ec5e
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