VCFtools vcf-consensus error

[jeffseq]

vcf-consensus fails to pick any variants in VCF file involing last position:

e.g. we have:

ref.fa:
>ref
ATCG

variants in ref.vcf:

ref 1 . A T . . .
ref 4 . G T . . .

when we do: cat ref.fa |vcf-consensus ref.vcf.gz
get:

>ref
TTCG

position 1 is OK but position 4, G->T is ignored.

Also, if we have:

ref 2 . TCG T . . .

TCG-> T deletion is also ignored. because G is the last position?

Any other good alternative tools to use (besides GATK, which I have other issues with it too)?

[chuanchao]

when I do: cat ref.fa |vcf-consensus ref.vcf.gz:

The fasta sequence does not match the REF at Y:2649856. g(cactta) in .fa, G in .vcf, frz=0