Use of 'chr' for chromosomes

molgenis / VaSeBuilder

Validation Set Builder

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Use of 'chr' for chromosomes #31

Closed MatthieuBeukers closed 5 years ago

MatthieuBeukers commented 5 years ago

Depending on the SAM/BAM/CRAM file, chromosomes can be preceded by 'chr' (e.g. chr21, chrX, etc)

TDMedina commented 5 years ago

Require a reference sequence, and check to make sure the reference sequences in the BAM/CRAM/VCF/etc. contain the same reference sequences. Otherwise, complain.

MatthieuBeukers commented 5 years ago

Fixed this with a check using the genome reference