Basic BED file not compatible with CNVkit batch

Question

[haydenshinn]

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:

[rpolicastro]

From the error you might have some lines with strand information (in the wrong column).

grep "[\+-]" input.bed

This would return any lines with strand info

[haydenshinn]

No output when running the grep command