Bedtools coverage confuses chromosomes

Question

[wsciekly.maciek]

I have a problem running bedtools coverage (bedtools v2.26.0 ): my bed file is:

9   137618991   137619028   EHMT1   0   +  
Y   14056216    14056289    VCY1B   0   +

and my Genome File is:

1   248956422
10  133797422
11  135086622
12  133275309
13  114364328
14  107043718
15  101991189
16  90338345
17  83257441
18  80373285
19  58617616
2   242193529
20  64444167
21  46709983
22  50818468
3   198295559
4   190214555
5   181538259
6   170805979
7   159345973
8   145138636
9   138394717
GL000194.1  191469
GL000213.1  164239
KI270711.1  42210
KI270721.1  100316
KI270727.1  448248
KI270728.1  1872759
KI270734.1  165050
X   156040895
Y   57227415

Yet when I try to run bedtools coverage -sorted I get: Error: requested chromosome MT does not exist in the genome file notebook_resources_LARP7_transcription/GRCh38.dna.primary_assembly.Genome_File.txt. Exiting.
Did anyone else encounter this?
I know that it is the second line in the bed file that is a problem. The first runs through...

===========
My command is:

bedtools coverage -sorted -a bed -b bam -g Genome_File.txt > out.tsv;

[finswimmer]

Hello,

please show us the complete command you are running.

Thanks.

fin swimmer

[Jeffin Rockey]

It should be just that the bed file has mitochondria entry whereas the genome file do not have an entry regarding that.

[wsciekly.maciek]

I have added the command above; Well, it should be but my bed file does not have MT entries...

[Jeffin Rockey]

Check the separators. MT is there in EHMT1 . Is the bed made in a Windows machine or so?

If so dos2unix might help

Also what about GRCh38.dna.primary_assembly.Genome_File.txt ?

Answer 1

[ATpoint]

The header of the BAM file most likely contains MT. Simple add it to the genome file. You can check with samtools view -H your.bam. To make genome files that match BAMs, you can do:

## requires indexed BAM file:
samtools idxstats your.bam | cut -f1-2 | grep -v '\*' > Genome_File.txt