Re: [Samtools-help] incorrect reference bases

[Thomas W. B. <tb...@um...>]

I'm guessing that these are IUPAC ambiguity codes for cases where 
the indel overlaps a SNP in other individuals, or the other allele 
in the same individual.  Look in the bcftools documentation for 
ways to suppress the ambiguity codes.  I don't know if there is 
a way or not.

 	 	 	 	 	 	-  tom blackwell  -

On Fri, 22 Jul 2016, Annie Cowell wrote:

> Hello,
>
> I'm calling variants the following way for single or multiple samples using
> samtools and bcftools version 1.3.1
>
> samtools mpileup -C50 -Bug -t AD -Q10 -f my.fasta sample.bam | bcftools
> call -mv -Ov > my.vcf
>
> However, I am getting unusual bases for a couple of indels in the reference
> field, such as W (as below) and R.
>
> AAKM01000065 8883 . GGW G 228 .
> INDEL;IDV=40;IMF=0.888889;DP=45;VDB=0.880501;SGB=-0.692976;MQSB=0.114162;MQ0F=0;AC=2;AN=2;DP4=0,0,8,18;MQ=49
> GT:PL:AD 1/1:255,78,0:0,26
>
> What causes this and how do I fix it?
>
> Thank you,
> Annie
>