Updated analysis: Subset manta FILTER=="PASS" consensus cnv

[kgaonkar6]

What analysis module should be updated and why?

Add a FILTER==PASS for manta calls used in copy_number_consensus_call. I think this filter is necessary so that we use a subset of high-confidence broad SVs called by manta. https://github.com/Illumina/manta/blob/master/docs/userGuide/README.md#vcf-format-fields

What changes need to be made? Please provide enough detail for another participant to make the update.

Add a filter to only keep calls where FILTER=='PASS'
$11 == 'PASS'
here

What input data should be used? Which data were used in the version being updated?

pbta-sv-manta.tsv.gz

When do you expect the revised analysis will be completed?

1day

Who will complete the updated analysis?

@kgaonkar6

[jharenza]

closed with #1114 #1115 #1116