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2.4.4 Call SNPs from alignment blocks and export to VCF file

The VcfOutput filter call SNPs from each block and output them to a VCF file. Only substitutions are called for now.


maf.filter=                                 \
    VcfOutput(                              \
        file=snp.vcf.gz,                    \
        compression=gzip,                   \
        reference=Ref,                      \
        genotypes=(sample1,sample2),        \
        all=no),                            \



A file path for the output VCF file.


Compression format for output file.

reference={species name}

A species name corresponding to the sequence to use as reference.

genotypes={list of species}

A list of species for which genotypes informations should be written. If not, void, a ’FORMAT’ column will be added to the output, as well as oneextra column per species to genotype. If the species is not present in this particular, or if a N or Gap is present, a dot (’.’) will be written in the column. Please note that species should be unique in each block, otherwise an error will occur.


If set to ’yes’, also output non-variable positions in the VCF file.