implement compressing vcfs by gatk, and flag to disable

NationalGenomicsInfrastructure / piper

A genomics pipeline build on top of the GATK Queue framework

9 stars 9 forks source link

implement compressing vcfs by gatk, and flag to disable #68

Closed b97pla closed 8 years ago

b97pla commented 8 years ago

by default, have GATK gzip-compress vcf files
compression can be skipped with the --skip_vcf_compression flag to the DNABestPracticeVariantCalling.scala workflow

b97pla commented 8 years ago

@johandahlberg here we go..

johandahlberg commented 8 years ago

Looks good to me. The only thing that I can thing of is that I'm not 100% sure it's necessary to have a skip option for the compression. I have a very hard time coming up with a case where it should actually be skipped. Let me know what you think and I'll merge.

Great work!

b97pla commented 8 years ago

you're probably right, I just wanted to have an option of using the "old" behavior. I suggest to merge with this option since it's already implemented