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Samtools Mpileup With Refrence Addition

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!

mpileup vcf
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updated by Ram Ram • written by Tiffani • Tiffani

1 answer

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.

• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

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