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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 sorted-millsbcf
vt view -h -w 10000 mills.bcf
vt view -h -w 10000 mills.bcf -o sorted-mills.bcf
#views mills.bcf and outputs to c1-mills.bcf with a compression level of 1. By default,
#the compression level is 6 where lower levels compress the file less but are faster.
#The difference in compression for BCF files between level 1 to level 9 is about 5% of
#of a level 1 compression file. The difference in time taken is about an additional 50%
#of a level 1 compression. The levels range from 0 to 9 where 0 means no compression
#but the file is encapsulated in bgzf blocks that allows the file to be indexed. A special
#level -1 denotes an uncompressed BCF file that is not encapsulated in bgzf blocks and
#are thus not indexable but are highly suitable for streaming between vt commands.
vt view -h mills.bcf -c 1 -o c1-mills.bcf
#views mills.bcf and selects variants that overlap with the regions found in dust.bed from chromosome 20
#views mills.bcf and selects variants that overlap with the regions found in dust.bed from chromosome 20
-r right window size for overlap []
-r right window size for overlap []
-l left window size for overlap []
-l left window size for overlap []
-c compression level 0-9, 0 and -1 denotes uncompressed with the former being wrapped in bgzf. [6]
-t bed file for variant selection via streaming []
-t bed file for variant selection via streaming []
-I file containing list of intervals []
-I file containing list of intervals []
