bedtools not working with gff from flybase

Question

[asif.zubair]

Hi,

I got a gff file from flybase that i am trying to use with bedtools. However, it is throwing an error:

(0)> bedtools intersect -a my.vcf -b dmel-2L-r5.41.gff
Error: Invalid record in file dmel-2L-r5.41.gff. Record is 
2L      FlyBase chromosome_band -204333 1326937 .       +       .       ID=band-21_chromosome_band;Name=band-21

I downloaded the gff from here

I don't know why this format would be incorrect. From what I know of gff files, it seems correct.

Any help would be appreciated.

Thank you,
Best,

asif

[Sam]

Why's your start coordinate negative?

Answer 1

[asif.zubair]

Yes, it turns out there is a problem with flybase's gff file. It seems flybase people fixed that in a newer version.

Thank you for pointing it out!