Question: Weird Samtools Mpileup Error In Mplp_Func.
gravatar for Shellfishgene
7.1 years ago by
Shellfishgene50 wrote:


What is samtools mpileup trying to tell me with this error (or warning):

[mplp_func] Skipping because 298 is outside of 0 [ref:103424]

There are many like it. I double checked that I have the same reference fasta in the mpileup and the actual bwa mem mapping commands, and I do.


samtools mpileup error • 2.2k views
ADD COMMENTlink modified 3 months ago by Emad0 • written 7.1 years ago by Shellfishgene50
gravatar for Sam
7.1 years ago by
New York
Sam3.3k wrote:

Reading the samtools mailing list using google found this:

Basically, what it is doing is exclude reads outside of the reference sequence From what the error is saying, it seems like your reference id 103424 has length of 0, therefore all the reads were excluded (I am guessing that the id is not exactly what you will see in your reference. It might be the internal index id of your reference, but I am not sure about that...)

ADD COMMENTlink written 7.1 years ago by Sam3.3k
gravatar for ketilm417
6.5 years ago by
ketilm41710 wrote:

I got this when mapping reads with bwa 0.6.2 (0.7.5 would segfault on certain files), and all reference sequences appear to be incorrectly mapped in the mpileup file after this occurs. It seems to be a bug either in bwa (producing an incorrect BAM file), or in samtools mpileup. Probably the latter, since examining the alignments with samtools tview doesn't reveal anything out of the ordinary.

This is such a mess: I can look at each of the BAM files with tview, and they look perfectly all right. But mpileup on the whole files fail, and if I try to look at the troublesome reference sequence (using -p to specify region), it only works for one of the files - the one which comes out incorrectly in the combined mpileup...

ADD COMMENTlink modified 10 months ago by RamRS30k • written 6.5 years ago by ketilm41710
gravatar for Emad
3 months ago by
Emad0 wrote:

Use exactly the same references in the bwa and mpileup.

ADD COMMENTlink written 3 months ago by Emad0
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