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kircherlab / CADD-SV

CADD-SV – a framework to score the effect of structural variants
https://cadd-sv.bihealth.org
MIT License
14 stars 3 forks source link

Bed file must be sorted #3

Closed andrewSharo closed 3 years ago

andrewSharo commented 3 years ago

Thanks for developing this method!

I ran CADD-SV locally on a bed file and received the following error

Error: Sorted input specified, but the file beds/chrs1357/chrs1357_wchr.bed has the following out of order record
chr7    72576419        72815631
Error: Sorted input specified, but the file beds/chrs1357/chrs1357_wchr.bed has the following out of order record
chr7    72576419        72815631

It appears that it requires a sorted bed file. Indeed, using a sorted bed file solved the problem.

I would recommend mentioning this in the ReadMe file, just because the snakemake output requires a lot of scrolling to get to the original error, which could trip up some folks.

Best, Andrew

frequena commented 3 years ago

I completely agree! A mention about it would be very helpful

kleinertp commented 3 years ago

Thanks for the hint,

I added this information in the manual