nonamecheck not working in bedtools coverage

Question

[roalva1]

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

Answer 1

[finswimmer]

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'

[roalva1]

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".

[GenoMax]

Are you mixing and matching the genomes by any chance? BED file from one provider where as BAM aligned to a different one?

[roalva1]

No no, I have got just a bam

[finswimmer]

Hm, I don't know what -nonamecheck does behind the scene.. Maybe it just ignores lower/upper cases and leading zeros?

genomax suggested to me, that it also could be a naming mismatch between the bam file and your bed file. How is the name for chrM in the bed file? Maybe chrMT or just MT.?

fin swimmer

[roalva1]

My bed file doesn't have any region in chrMT nor chrM

[GenoMax]

Interesting. Then why are you getting this? Or you just don't have any chrM regions in your bed file (and that is just a warning).

Database file file.bam contains chromosome chrM, but the query file does not.

[roalva1]

Yes, I don't have any chrM regions in my bed file, but I do have in my bam. The message of bedtools should be a warning but it is not. Bedtools stops and the coverage in chrX regions are not calculated.

[roalva1]

This has solved my problem, but still, with bedtools 2.17 we didn't need this, and I think it is not intuitive.

[GenoMax]

You can accept @fin swimmer's answer (green check mark) to provide to closure to this thread since your problem is solved.