Warning: This suite is under active development and this is not a stable nor well tested version. We are not able to provide user support for this version of svtools.
svtools: comprehensive utilities to explore structural variations in genomes.
Hall-lab
$Revision: 0.0.1 $
$Date: 2015-10-14 14:31 $
usage: svtools <subcommand> [options]
The svtools sub-commands include:
[ general utilities ]
vcftobedpe converts vcf file into bedpe.
bedpetovcf converts bedpe file to vcf.
bedpetobed12 converts bedpe file to bed12.
vcfsort sorts a vcf file.
bedpesort sorts a bedpe file.
[ callset generation ]
prune cluster a BEDPE file by position based on allele frequency.
varlookup look for variants common between two bedpe files.
afreq add allele frequency information to a VCF file.
lsort sorts a vcf file by type.
lmerge merges multiple sorted vcf files.
genotype return a vcf file with genotype information added by svtyper.
copynumber add cn information using cnvnator.
vcfpaste combine multiple vcf files produced by genotype command.
classify classify structural variants
[ General help ]
--help print this help menu.
--version what version of svtools are you using?.
--contact feature requests, bugs, mailing lists, etc.
URL https://github.com/hall-lab/svtools
Note: For additional information and usage refer to the svtools_demo.sh file.