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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), \
[...]
|
file={none|{path}}A file path for the output VCF file.
compression={none|gzip|zip|bzip2}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.
all={boolean}If set to ’yes’, also output non-variable positions in the VCF file.