GenomeComb

correctvariants

Format

cg correctvariants ?options? varfile resultfile dbdir

Summary

Complete or correct a variants file

Description

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.

Arguments

srcfile
variations file
dstfile
resulting variations file
dbdir
database directory with reference sequence, etc.

Options

-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.

Category

Conversion