Description Usage Arguments Value
View source: R/preProcessSnvIndel.R
Wrapper function for SnpSift filter and SnpSift intervals. Selects PASS variants and variants at coords specified in bed file. For germline vcfs, remove somatic variants.
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vcf.file |
Path to vcf file (gzip compressed) |
out.file |
Path to output vcf file (make sure to add .gz at the end) |
mode |
Can be 'germ' or 'som' |
bed.file |
Path to bed file specifying the genome intervals to keep (defaults ot the one stored in this package) |
java.path |
Path to java binary (defaults to the installed JRE location) |
snpsift.path |
Path to SnpSift jar (defaults to the one included in this package) |
Nothing but writes a gzipped vcf file
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