[Samtools-help] incorrect reference bases

[Annie C. <ann...@gm...>]

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