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?

Edit:

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.