tsivaarumugam

Hard coded additional GC content filter in fix.py module

3

Hello, In cnvkit version 0.9.8 and above, there is a hard coded GC content filter at line number 125 in the **"mask_bad_bins"** definition in fix.py module [commit](https://github.com/etal/cnvkit/commit/2e6a40a6664f60cd6743b0c86c917ce4c33c7ab0). I understand the...

Dear Team, We are trying to run the Pangolin tool with one of the GiaB (Genome in a Bottle) WGS sample VCF file. Is there a system configuration recommendation for...

Pangolin exits with error if variant with wildcard character

1

Hi Team, While using a VCF file with wildcard character "*" in the allele field [Spanning-or-overlapping-deletions-allele](https://gatk.broadinstitute.org/hc/en-us/articles/360035531912-Spanning-or-overlapping-deletions-allele), Pangolin exits with error. Example entry: 3 60539233 . AAAATATAT AATAT,* 550 PASS ....