I have an alignment file for a protein encoded by about ~3000 bases (I have both bam and sam files), and I am looking to extract all the reads that from bases 877-981. Is there any way to do this with samtools?
I tried using this command:
samtools view 8.2alnCorrected.bam "877-981" > filteredreads.bam
However I got this message with an empty file:
region "877-981" specifies an unknown reference name. Continue anyway.
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michael.madans94 •
You need to specify the chromosome or contig as well. Your bam will have lines that look like:
chr1 12345 ...
So for reads are mapped to that chromosome or contig, you want:
samtools view 8.2alnCorrected.bam chr1:877-981
It worked out. Thanks Chris!
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michael.madans94 •
Glad to hear it! Consider hitting the "Accept" button next to the answer - that lets anyone else who stumbles across this question find the solution easily.
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Chris Miller
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Take a look at the manual to correctly specify the region (RNAME[:STARTPOS[-ENDPOS]]): http://www.htslib.org/doc/samtools.html