cg correctvariants ?options? varfile resultfile dbdir
Complete or correct a variants file
This command adds ref and alt fields to a variation file that
misses them, and fills them. The alt field wil also be updated based
on the alleleSeq* genotype fields if these are present in the variant
file. If a ref fields is already present, its contents will be
checked, and an error given if there is a difference with the genome
sequence in dbdir. The -f (force) or -c (complement) option can be
used to correct the ref column instead of giving an error.
- variations file
- resulting variations file
- database directory with reference sequence, etc.
- -f 0/1/2
- if 1 (default 0), force overwrite of ref if it is different
from the genome sequence in dbdir, instead of giving an
error. "alt", "sequenced" and "zyg"
columns are also corrected to reflect the new reference. Use
"2" to give a warning on the changes
- -c 0/1
- if 1 (default 0), overwrite ref if it is different from the
genome only when it is complement of ref, alt and alleleSeq* are
also changed to complement if ref is complement. This option is
usefull for data originally coming from e.g. a snp array where
variants are sometimes given in the reverse strand.
- -s 0/1
- if 1 (default 0), the file is interpreted as a variant file
with split alternative alleles (i.e. each alternative allele of a
SNV is on a separate line as a seperate variant). This means e.g.
that the alt column will not be updated based on genotypes present.