Somatic Variant Reporting support for GRCm38 about genome HOT 2 CLOSED

WIP : https://github.com/jasonwalker80/genome/tree/grcm38_somatic_reports

from genome.

A snippet of notes on the remaining issue of a missing CAF field in the VCF that is expected by the reporting framework:

jwalker [3:34 PM]
I'm attempting to run a basic report through the Variant Reporting Framework. I removed all human specific annotations and switched appropriate values to GRCm38 and mus-musculus

[3:35]
I ran into an issue where both CAF and MUT were not defined INFO fields in the dbSNP VCF. I removed CAF but the 'full' report seems to expect caf. Here is the error after removing all caf references from the plan_file :

jwalker [3:35 PM]
added a Plain Text snippet
2016/11/02 15:28:58 Genome::VariantReporting::Framework::Plan::MasterPlan id(linus2112.gsc.wustl.edu 11204 1478118523 10005): Property ["caf"]: Interpreters required by report (full) but not provided: (caf)
ERROR: Property ["caf"]: Interpreters required by report (full) but not provided: (caf)
2016/11/02 15:28:58 Genome::VariantReporting::Framework::Plan::MasterPlan id(linus2112.gsc.wustl.edu 11204 1478118523 10005): Failed to validate
ERROR: Failed to validate
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susannakiwala [3:37 PM]
what happens when you put caf: {} in the plan_file?

jwalker [3:38 PM]
added a Plain Text snippet
2016-11-02 15:08:48-0500 blade12-1-11: DEBUG: Processing (/gscmnt/gc13001/info/model_data/software-result/35befa0df01e4b8c9bd0cdc708bd4500/joinx_vcf_annotate.vcf.gz) entry by entry
2016-11-02 15:08:59-0500 blade12-1-11: 2016/11/02 15:08:59 Genome::VariantReporting::Framework::GenerateReport id(blade12-1-11.gsc.wustl.edu 13406 1478117319 10002): Exception in execute: INFO tag CAF not found in VCF header at /gscmnt/gc13001/info/model_data/jwalker_scratch/genome/lib/perl/Genome/File/Vcf/DbsnpAFParser.pm line 13, line 11486.
2016-11-02 15:08:59-0500 blade12-1-11: ERROR: Exception in execute: INFO tag CAF not found in VCF header at /gscmnt/gc13001/info/model_data/jwalker_scratch/genome/lib/perl/Genome/File/Vcf/DbsnpAFParser.pm line 13, line 11486.
2016-11-02 15:08:59-0500 blade12-1-11: Failed to execute for command Genome::VariantReporting::Framework::GenerateReport. at /gscmnt/gc13001/info/model_data/jwalker_scratch/genome/lib/perl/Genome/Ptero/Wrapper.pm line
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jwalker [3:38 PM]
The mouse dbSNP VCF does not have CAF defined in it

[3:38]
hence the annotated VCF doesn't have it in the header either

from genome.