Samtools Mpileup With Refrence Addition

Question

[Tiffani]

Hello, ever since the new update, when I run samtools mpileup in the pipeline I recieve this output:

1    5653502    .    A    G,X    64    .    
1    5653513    .    T    C,X    64    .    
1    5653515    .    G    A,X    64    .    
1    5654969    .    T    C,X    54    .    
1    5655208    .    G    A,X    14.2    .    
1    5655225    .    C    T,X    14.2    .    
1    5657398    .    C    T,X    23.4    .    
1    6877349    .    C    A,X    30    .    
1    7637651    .    C    T,X    24.1    .    
1    7672096    .    G    A,X    51    .

I'm wondering why it has $variant,X now, it's never had that before, any answers would be greatly appreciated.

Thanks!

Answer 1

[Pierre Lindenbaum]

in the documentation: http://samtools.sourceforge.net/mpileup.shtml

In the BCF generated by SAMtools, an non-ref base 'X' represents an base has not been seen from the alignment data. Such a base is necessary to evaluate the probability of missing a non-ref allele due to sampling fluctuation.

[Michi]

Do you know how to remove this non-ref allele if not desired in the output?

EDIT for future readers: I asked in a separate question: Mpileup BCF/VCF output without non-ref base 'X'?