check for the chrom names in the input vs dbSNP & reference fasta

[darked89]

Hello,

Would it be possible to add an extra check for chr name in the gwas/TSV input not present in the genomic fasta and/or dbSNP file?
I am aware that this is handled by the alias file/switch, so it may be redundant.
Nevertheless I was quite puzzled by:

 Variants discarded during harmonisation: 537691

Getting a line stating: "WARNING: chromosome(s) 23 and barfoo not present in Fasta: path_to_fasta_file" will make things easier to debug.

Hope it helps,

Darek Kedra

[mcgml]

great suggestion, thanks @darked89. I will add soon