Snowman VCF Visualisation in IGV about svaba

[walaj]

Hi Tunc,

The ICGC indel calls were made from a much earlier version (~18 mo ago) that did not fill in the genotype fields, but instead put the tumor / normal read counts in the INFO field. This has been fixed for some time, but the ICGC data is frozen in the old format. For visualization in IGV, it does seem that removing the headers that mark empty genotype fields is the best way to go.

[mortunco]

Dear Jeremiah,

Thank you for the rapid response.

that did not fill in the genotype fields, but instead put the tumor / normal read counts in the INFO field I see this info kept by putting N/T prefix in to the measure. Since I am also interested in the homogeneity of the mutation, by which measure should I calculate if that mutation is homozygous or heterozygous. or Is it any possible ?

Best regards,

Tunc.

[walaj]

Hi Tunc,
Apologies for the slow response. Genotype calculations in SvABA (was snowman) are calculated using eqn 2 of https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3198575/

However the version you have did not have genotype calculations, so indeed you would have to implement eqn 2 manually, using the REF and ALT counts.

[walaj]

Closing since this is outdated relative to much newer versions.