Hi all,
I was trying to find the inward oriented pairs (innies) and outward oriented pairs (outties) using Bamcheck and Samtools. Both gave me different results on running. May I know which one to pick from both? Any suggestions or comments are welcome!
I will answer this question myself. I was continuously trying to test this, on a small .bam file as @Devon has suggested.
Finally,
samtools stats seems to be giving me correct results.
I have done this by converting bam file to bed file, and then took the reads coordinates, along with orientations and counted the number of inward and outward pairs. As a side point, It appears that that samtools will also take care of an extra step that if it finds two reads in a pair (either innie or outtie) to be overlapping, it ignores them and does not report as either inward pair or outward pair, although by direction they are either facing (--> <--) or not facing other (<-- -->).
I have looked outward pairs in a third party visualization tool called tablet, which showed them as outward and improperly paired.
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On the other hand,
bamcheck failed to recognize any outward pairs from my bam file (which can be noticed from the screenshot in the question).
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version 2.3.6
My guess would be that these are handling dovetailed and or bookended reads differently. Since the files are small, just subset them until you find a single alignment that causes the numbers to differ and then have a look at that.
Thanks Devon Ryan. I will try to look at that. May I know what it means by dovetailed and bookended reads?
That nomenclature is borrowed from bowtie2, though I probably meant "contain" rather than "bookend".