Coordinates for Structural Varinats in DR (post-release small issues)

[TimHHH]

// GATK_SELECT_VARIANTS__INTERVALS(GATK_INDEX_FEATURE_FILE.out, params.drgenes_list) in the CALL workflow is not yet enabled, is the -L ${intervalsFile} \\ available yet? Or should I create one?

[abhi18av]

I'm afraid that the drgenes_list file hasn't been added to the repo yet

https://github.com/TORCH-Consortium/xbs-nf/blob/6c29d1cb874357c1c89f566c40d65049765cb1bc/default_params.config#L55

As soon as we have file we can enable that process.

[TimHHH]

@LennertVerboven this file seems promising for this purpose: https://github.com/TORCH-Consortium/xbs-nf/blob/master/resources/resistance_db_who/resistance_db_who.bed
Do you know if the genes mentioned there are tier 1 and/or tier 2?

[TimHHH]

[abhi18av]

@TimHHH @vrennie @mdediegofuertes , given the recent work on structural variants, is this issue still relevant?

[vrennie]

I don't this is relevant anymore considering we are relying fully on TBProfiler for interpretation.

@mdediegofuertes thoughts?