'Excluded' variants

[rmpb94]

Hi everyone,
I've been trying to use the pgsc-calc pipeline with my data, and for the most part this has been working really well. I just have a bit of an issue with a SNP that has been 'excluded' according to the match data. Is there a way to find out why this SNP has been excluded, and to over-ride this to force it's inclusion?
Thanks,
Róisín

[smlmbrt]

Hi @rmpb94,

The variant will likely be excluded for one of the following reasons and one of the following flags/columns will == TRUE (see https://pgsc-calc.readthedocs.io/en/latest/output.html#match for latest documentation):

column	Description
is_multiallelic	True/False flag indicating whether the matched variant is multi-allelic (multiple ALT alleles). Default
ambiguous	True/False flag indicating whether the matched variant is strand-ambiguous (e.g. A/T and C/G variants).
duplicate_best_match	True/False flag indicating whether a single scoring file variants has multiple potential matches to the target genome. This usually occurs when the variant has no other_allele, and with variants that have different REF alleles.
duplicate_ID	True/False flag indicating whether multiple scoring file variants match a single target ID.

Most of these behaviours can be altered using flags in the command line (https://pgsc-calc.readthedocs.io/en/latest/reference/params.html), for instance --keep_multiallelic and--keep_ambiguous.

[rmpb94]

Great, thanks! I'll investigate and run with the relevant flags.
Thank you!