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)?
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)?
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