I'm trying to plot the depth of coverage but when running samtools depth it seems to skip over bases which I presume have no alignments spanning those regions. However, it does report some bases where there are no alignments, though few and it nowhere near compensates for the bases that it omits.
After grepping through the file the number of bases for the reference provided by samtools depth is always less then the actual number of bases. I made sure that there would be no character incompatibilities (Ns etc.) and still no improvement. Has anyone noticed this before? Is this a bug or does it just not display positions with no alignments?
I'm using samtools version 0.1.18 (r982:295) and produced bam files from both SHRiMP and Bowtie.
After grepping through the file the number of bases for the reference provided by samtools depth is always less then the actual number of bases. I made sure that there would be no character incompatibilities (Ns etc.) and still no improvement. Has anyone noticed this before? Is this a bug or does it just not display positions with no alignments?
I'm using samtools version 0.1.18 (r982:295) and produced bam files from both SHRiMP and Bowtie.
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