nonamecheck not working in bedtools coverage

Question: nonamecheck not working in bedtools coverage

9 months ago by

Spain

roalva1 • 80 wrote:

Hello,

I am running this command line in bedtools 2.27.1

bedtools coverage -nonamecheck -d -sorted -a file.bed -b file.bam  > file.cov

and I get this error

ERROR: Database file file.bam contains chromosome chrM, but the query file does not.
       Please rerun with the -g option for a genome file.
       See documentation for details.

I don't have access to the genome file and I guess nonamecheck is not working,

Thanks a lot

Best regards

bedtools • 374 views

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modified 9 months ago by RamRS ♦ 21k • written 9 months ago by roalva1 • 80

9 months ago by

finswimmer ♦ 11k

Germany

finswimmer ♦ 11k wrote:

Hello,

the genome file is need if you want to use -sorted. You can extract this information from your bam file as all informations are in the header.

$ samtools view -H file.bam|grep @SQ|sed 's/@SQ\tSN://'|sed 's/LN://' > genome.txt

fin swimmer

(I'm sure there is more beautiful sed command ;) )

Edit: Just for documentation the sed commands can be combined in one:

sed 's/@SQ\tSN:\|LN://g'

ADD COMMENT • link modified 9 months ago • written 9 months ago by finswimmer ♦ 11k

Wouldn't be -nonamecheck enaugh for this?

-nonamecheck    For sorted data, don't throw an error if the file has different naming conventions
        for the same chromosome. ex. "chr1" vs "chr01".