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Also, in the same module, I think it will be useful to add an optional argument to enable using t_depth values present in the maf file directly for calculating t_var_freq, instead of calculating t_depth as t_alt_count + t_ref_count. This is because:
1.) In multi-allelic sites, calculating t_depth as t_alt_count + t_ref_count might be incorrect.
2.) Although rare, in some input maf files, only the t_depth and t_alt_count columns are populated. This causes NA to be coerced for all columns related to ccf.
I made the update above for my usage. If this of any interest to you, I'm happy to do a PR.
The text was updated successfully, but these errors were encountered:
Hi,
There is a minor error here: https://github.com/mskcc/facets-suite/blob/master/R/ccf-annotate-maf.R#L29. The check is for the presence of
t_alt_count
andt_ref_count
columns, but the error message is "Columnst_alt_count
andt_depth
required."Also, in the same module, I think it will be useful to add an optional argument to enable using
t_depth
values present in the maf file directly for calculatingt_var_freq
, instead of calculatingt_depth
ast_alt_count
+t_ref_count
. This is because:1.) In multi-allelic sites, calculating
t_depth
ast_alt_count
+t_ref_count
might be incorrect.2.) Although rare, in some input maf files, only the
t_depth
andt_alt_count
columns are populated. This causes NA to be coerced for all columns related to ccf.I made the update above for my usage. If this of any interest to you, I'm happy to do a PR.
The text was updated successfully, but these errors were encountered: