I'm using this series of commands to get consensus sequences:
samtools mpileup -vf seqs.fa aligned.bam > vcf.gz tabix -p vcf -f vcf.gz cat seqs.fa | vcf-consensus vcf.gz > consensus.fa
(I was trying to do this using bcftools/vcfutils.pl but was having a different problem I've finally given up on)
I'm getting this error:
The fasta sequence does not match the REF at XLOC_000009.TCONS_00000016:733. G(GTTATA) in .fa, C in .vcf, frz=0
but if I check the fasta sequence using samtools faidx, it gives the C that's expected:
$ samtools faidx seqs.fa XLOC_000009.TCONS_00000016:733 >XLOC_000009.TCONS_00000016:733 C
These warnings from before the error might be relevant?
The version "4.2" not supported, assuming VCFv4.1 Note: Conflicting variants at (or near) XLOC_000009.TCONS_00000016:725, cannot apply both.
Does anyone know why I'm getting this error and how to fix it?
The line in the vcf at this location is:
XLOC_000009.TCONS_00000016 733 . C <*> 0 . DP=14;I16=0,8,0,0,222,6594,0,0,336,14112,0,0,0,0,0,0;QS=1,0;MQ0F=0 PL 0,24,128
I noticed it's the last line/position for that sequence.