[ Failed Analysis ] CNVpytor float values not accepted by bcftools

[mathiasbio]

Case or sample information
Internal sample id or case id: modelstag
Amount read-pairs: 2688801506
Sequence type (WGS): Tumor only

Error message
Rule that failed: bcftools_quality_filter_svdb

Error message:

[W::bcf_hdr_parse_line] Dropped trailing junk from header line '"##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">;"'
[E::vcf_parse_format] Invalid character '.' in 'CN' FORMAT field at 8:35400001
[E::vcf_parse_format] Invalid character '.' in 'CN' FORMAT field at 8:46900001
Error: VCF parse error

Link to the error message

/home/proj/production/cancer/cases/modelstag/logs/BALSAMIC.modelstag.bcftools_quality_filter_svdb.6.sh_4695700.err

Reason for failure

CNVpytor outputs float values for CN sometimes:
8 35400001 CNVpytor_dup8 . . PASS INFOfieldremoved GT:CN ./1:2.73

Don't know if this is intentional or a bug from CNVpytor!

If workflow, which rules

bcftools_quality_filter_svdb in WGS tumor only

Version (please complete the following information):
balsamic --version 11.0.2

Additional context
Add any other context about the problem here. For e.g. amount sequencing reads or other parameters that are of interest.

[pbiology]

@mathiasbio can you assign gain/urgency/effort labels to this?

[pbiology]

Or was this solved by #1183 and #1182 ?

[khurrammaqbool]

It was fixed in CNVpytor abyzovlab/CNVpytor#178 and we have added the latest version of CNVpytor in develop.

[mathiasbio]

I didn't know about the CNVpytor update fixing it, that's great. I guess my fix is unnecessary then at this point, did you remove the sed command I added @khurrammaqbool ? I guess it doesn't matter if it's there either, but it would be cleaner if we removed it I suppose when it's not necessary anymore : )

[mathiasbio]

Removed the sed command in #1310 and as the issue has already been solved in the CNVpytor update I'll close this issue