Coverage information of the read using samtool
Hi, I want to obtain coverage information of the read using samtool. I gave the following command- ./samtools stats -c mappedreversecomp.bam . I got an error "Unable to parse -c mappedreversecomp.bam" Kindly help in identifying the mistake.
Thanks Madhu
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2 answers
- It's
samtools, not "samtool" - Unless you're operating out of a directory where both the
samtoolsbinary and the filemappedreversecomp.bamare both accessible, you're doing it wrong. You should be in the directory that has the BAM file andsamtoolsshould be in your$PATH, with you executingsamtools stats -c ./mappedreversecomp.bam - Please format your question better. Use the code button to your advantage.
If you're using Ubuntu, use sudo apt-get install samtools to install samtools. cd to your directory that has the BAM file and then use the command I mentioned above.
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The help is the first place you should look:
$ samtools stats
About: The program collects statistics from BAM files. The output can be visualized using plot-bamstats.
Usage: samtools stats [OPTIONS] file.bam
samtools stats [OPTIONS] file.bam chr:from-to
Options:
-c, --coverage <int>,<int>,<int> Coverage distribution min,max,step [1,1000,1]
Looks like samtools stats is expecting 3 numbers to follow the -c. You didn't put any.
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Madhu,
Please follow genomax's advice and do the following for your questions:
If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.