| Hi, I’ve found something very strange with samtools mpileup, looks like a bug. If I provide the reference fasta I get completely different results than if I don’t. Look at this example:
Now look what we get if we do not provide a reference:
For site 36052981, if I provide the reference only two bases are reported, whereas without the reference 11 bases are found. Note that quality bases also change. I checked with IGV that the second case is the correct one (see snapshot). Interestingly, all but two of the reads that overlap 36052981 have an indel three bases before, so I guess the bug may be related to this. I am attaching a very small bam of the region. If it helps diagnosing the problem I can send more information for other “strange” cases. Regards, Federico |
caca.bam
Description: Binary data
smime.p7s
Description: S/MIME cryptographic signature
------------------------------------------------------------------------------ What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. http://sdm.link/zohomanageengine
_______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
