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. |
chromosome |
Name of the column containing chromosome names in the specified input file. |
id |
Name of the column containing SNP identifiers in the specified input file. |
alleles |
Vector with column names containing reference and non-reference alleles in the specified input file. |
sep |
The field separator character in the specified input file. |
vcf_alleles |
When applicable, alleles in the input file are recoded to R(reference)/I(insertion)/D(deletion) format. If vcf_alleles is set to TRUE, then alleles are recoded based on the VCF reference. Otherwise, alleles are recoded using only information available in the 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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