Add DoCM genotyping about analysis-workflows HOT 3 CLOSED

I believe you can download the DoCM variants in VCF format here:
http://docm.genome.wustl.edu/

Those coordinates will be GRCh37. I'd suggest running:
https://broadinstitute.github.io/picard/command-line-overview.html#LiftoverVcf

See an example of using the LIftoverIntervalList tool for HCC1395 analysis, section Picard LiftoverIntervalList:
https://github.com/griffithlab/precision_medicine_workshop/blob/master/Introduction.md

The above example includes the path to the chain fail on MGI filtesystem where $SOMATIC_HOME=/gscuser/jwalker/git/HCC1395/arvados

My first suggestion is to run the GATK HaplotypeCaller using the --genotyping_mode=GENOTYPE_GIVEN_ALLELES option.

Ideally we would simply add the output VCF to the GATK CombineVariants step as another variant caller, ex. 'GATK-HC-DoCM'

from analysis-workflows.

A possible solution to the filter issue, write our own:
https://github.com/arq5x/cyvcf

from analysis-workflows.

PR #111 closed this.

from analysis-workflows.