Brad Chapman

Matt; Apologies, this hasn't gotten much development time in a while due to changing priorities so is not super active. It looks like we'd need to re-set up the hosting...

Tim; Yes. There are some facilities to make it easier to deal with human data but you should be able to do comparisons with any set of variants and reference...

Sakina; It sounds like something is problematic with your Genome in a Bottle file since both GATK and bcftools are complaining about it. You could use the one we distribute...

Thanks very much for catching this issue and for the fix. There is a new 0.7.0 release on pypi that contains this fix. Apologies again about being slow to get...

Erik; Sorry about this. I moved these over to another repository. The new wgets are: ``` wget https://github.com/chapmanb/bcbio.variation.recall/raw/master/test/data/ensemble/NA12878-10.bam wget https://raw.github.com/chapmanb/bcbio.variation.recall/master/test/data/ensemble/chr10-start.fa ``` Please let me know if you run into anything...

Sorry about the issue -- it looks like Homebrew/Linuxbrew have migrated away from using sha1 and now force sha256. These recipes have fallen out of date as we don't use...

Sorry about the issues, the ngs_pipeline_minimal module should no longer be using Homebrew/Linuxbrew recipes. Would you be able to post the full error you're seeing so we can figure out...

Thanks for the full traceback. This looks like the install is using the default set of parameters instead of the `ngs_pipeline_minimal` one, which leads to the issue. You're right that...

Scott; Sorry about the continued problems. If you could make the FreeBayes file available that would be a big help to help diagnose further. This error indicates there is something...

Scott; Sorry about forgetting to respond to that. That's fine with the cavaet that MNPs also contain SNPs, just compressed together in haplotypes, so you'll miss those. If you've previously...