Extract lumpy PE & SU info from vcf and pass it through to ximmer local_combined_cnvs.json output

ssadedin / ximmer

Ximmer is a system for CNV calling on exome and targeted genomic sequencing

http://ssadedin.github.io/ximmer/

GNU Lesser General Public License v2.1

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Closed TacModd closed 3 months ago

TacModd commented 3 months ago

Currently PE, SU & SR info are summed together so cannot be filtered on individually
PE & SU are thus added separately under a new 'extrainfo' field
These are then passed through to the local_combined_cnvs.json output where they can be used for filtering
The 'extrainfo' field is available for all callers but will be passed through as an empty field if unpopulated

ssadedin commented 3 months ago

Looks good, thanks @TacModd