Need
As a researcher / clinician doing interpretation of CNVs from WGS analyses I would like to have access to:
- the BAF plots loaded into GENS but in a format accessible by IGV (because when working from home GENS can be too slow)
- the CNV.somatic.*.ascat.copynumber.txt.gz file but from the normal sample which can be useful to get the uniparental disomy
See freshdesk ticket with request: https://scilifelab.freshdesk.com/a/tickets/1000758
Suggested approach
It shouldn't be necessary to parse ascat to get the type of information that Teresita wants. If the only issue is slow GENS when working from home. It should be sufficient to parse the same files we use for GENS into a format useable in IGV.
- Add extra scripts to parse CNVkit and gnomad_af_vcf to bedgraph
Considered alternatives
No response
Deviation
No response
System requirements assessed
Requirements affected by this story
No response
Risk assessment needed
Risk assessment
No response
SOUPs
No response
Can be closed when
No response
Blockers
No response
Anything else?
No response
Need
As a researcher / clinician doing interpretation of CNVs from WGS analyses I would like to have access to:
See freshdesk ticket with request: https://scilifelab.freshdesk.com/a/tickets/1000758
Suggested approach
It shouldn't be necessary to parse ascat to get the type of information that Teresita wants. If the only issue is slow GENS when working from home. It should be sufficient to parse the same files we use for GENS into a format useable in IGV.
Considered alternatives
No response
Deviation
No response
System requirements assessed
Requirements affected by this story
No response
Risk assessment needed
Risk assessment
No response
SOUPs
No response
Can be closed when
No response
Blockers
No response
Anything else?
No response