Description Usage Arguments Author(s)
Function harmonizes SNP identifiers and alleles in the input file according to the provided VCF reference.
1 |
input |
Name of an input file. |
output |
Name of an output file. |
vcf |
Name of the VCF reference. |
id |
Name of the column containing SNP identifiers in the specified input file. |
chromosome |
Name of the column containing chromosome names in the specified input file. |
position |
Name of the column containing chromosomal positions in the specified input file. |
alleles |
Vector with column names containing first and second alleles in the specified input file. |
flip |
If TRUE, automatically flips alleles in order to match variant strand in VCF reference. Otherwise, the variant is considered as unresolved. |
sep |
The field separator character in the specified input file. |
drop |
If TRUE, then all unresolved variants are dropped from the output file. |
gzip |
TRUE if output file is in gzip format. |
Daniel Taliun, Christian Fuchsberger, Cristian Pattaro
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