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=== Mac ===
You may install vt via homebrew.
brew tap brewsci/bio
brew tap brewsci/science
brew install brewsci/bio/vt
Building has been tested on Linux and Mac systems on gcc 4.8.1 and clang 3.4. <br>
Some features of C++11 are used, thus there is a need for newer versions of gcc and clang.
= Updating =
= Updating =
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#converts in.bcf to tab format with selected INFO fields
#converts in.bcf to tab format with selected INFO and FILTER fields
vt info2tab in.bcf -v -t EX_RL,FZ_RL,MDUST,LOBSTR,VNTRSEEK,RMSK,EX_REPEAT_TRACT
vt info2tab in.bcf -u PASS -t EX_RL,FZ_RL,MDUST,LOBSTR,VNTRSEEK,RMSK,EX_REPEAT_TRACT
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INPUT
INPUT
OUTPUT
OUTPUT
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======
CHROM POS REF ALT N_ALLELE EX_RL FZ_RL MDUST LOBSTR VNTRSEEK RMSK EX_REPEAT_TRACT_1 EX_REPEAT_TRACT_2
CHROM POS REF ALT N_ALLELE PASS EX_RL FZ_RL MDUST LOBSTR VNTRSEEK RMSK EX_REPEAT_TRACT_1 EX_REPEAT_TRACT_2
20 17548608 A AC 2 2 13 1 1 0 0 17548608 17548608
20 17548608 A AC 2 1 2 13 1 1 0 0 17548608 17548608
20 17548608 AAAAG A 2 4 13 1 1 0 0 17548609 17548609
20 17548608 AAAAG A 2 1 4 13 1 1 0 0 17548609 17548609
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usage : vt info2tab [options] <in.vcf>
usage : vt info2tab [options] <in.vcf>
options : -v print variant CHROM,POS,REF,ALT,N_ALLELE [false]
options : -d debug [false]
-f filter expression []
-f filter expression []
-t list of info tags to be extracted []
-u list of filter tags to be extracted []-t list of info tags to be extracted []
-o output tab delimited file [-]
-o output tab delimited file [-]
-I file containing list of intervals []
-I file containing list of intervals []
