Basic BED file not compatible with CNVkit batch
I'm trying to run the batch command using a basic BED file that was downloaded directly from the Agilent website and CNVkit won’t parse it correctly. This is the error I'm getting for every line (respective to chromosome name):
Errors in BED line 'chrY\t57211760\t57211894\t-'\n
I double checked that it's tab separated and it only contains the chromosome name, start, stop but for some reason it still won't parse correctly.
Bed file head:
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haydenshinn •
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