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#views mills.bcf and outputs to standard out
#views mills.bcf and outputs to standard out
vt view -h mills.bcf
vt view -h mills.bcf
#views mills.bcf and locally sorts it in a 10000bp window and outputs to out.bcf
#views mills.bcf and locally sorts it in a 10000bp window and outputs to out.bcf
vt view -h -w 10000 mills.bcf
vt view -h -w 10000 mills.bcf
#views mills.bcf and selects variants that overlap with the regions found in dust.bed from chromosome 20
#the -t option selects variants by checking if each variant overlaps with the regions in the bed file, this is
#as opposed to random accessing the variants via the index through the intervals defined in -i and -I options.
#this is useful when selecting variants from the target regions from an exome sequencing experiment.
vt view 10000 mills.bcf -t dust.bed -i 20
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options : -o output VCF/VCF.GZ/BCF file [-]
options : -o output VCF/VCF.GZ/BCF file [-]
-f filter expression []
-w local sorting window size [0]
-w local sorting window size [0]
-s print site information only without genotypes [false]
-s print site information only without genotypes [false]
-h print header [false]
-H print header only, this option is honored only for STDOUT [false]
-h omit header, this option is honored only for STDOUT [false]
-p print options and summary []
-p print options and summary []
-r right window size for overlap []
-l left window size for overlap []
-t bed file for variant selection via streaming []
-I file containing list of intervals []
-I file containing list of intervals []
-i intervals []
-i intervals []
