Hi Annie,
As a way to avoid this problem we usually use a fasta file with no IUPAC
ambiguous codes (other than N) as reference for variant calling.
We'll take our standard reference without IUPAC codes, add IUPAC codes
based on dbSNP and then map reads to this with novoalign. In the variant
calli
On 22 Jul 2016, at 21:49, Annie Cowell wrote:
> 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.
>
> AAKM0165 8883.
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.
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,
