Bedtools coverage confuses chromosomes
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...
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My command is:
bedtools coverage -sorted -a bed -b bam -g Genome_File.txt > out.tsv;
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1 answer
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
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Hello,
please show us the complete command you are running.
Thanks.
fin swimmer
It should be just that the bed file has mitochondria entry whereas the genome file do not have an entry regarding that.
I have added the command above; Well, it should be but my bed file does not have MT entries...
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 ?