Chromosome notation standardisation (removing 'chr' string from chromosome names - mainly an issue in hg38 BAMs)

Chromosome notation standardisation (removing 'chr' string from chromosome names - mainly an issue in hg38 BAMs)

standardiseChrNotation(tumourname, normalname)

Arguments

tumourname

Tumour identifier, this is used as a prefix for the allele count files. If allele counts are supplied separately, they are expected to have this identifier as prefix.

normalname

Matched normal identifier, this is used as a prefix for the allele count files. If allele counts are supplied separately, they are expected to have this identifier as prefix.

Author

Naser Ansari-Pour (BDI, Oxford)