Sorry Pirrere, I have removed "$" before " sort" I did not use linux-sort, "> sort -k1,1d -T genome.dict -k2,2n" just pop up right away after i run "$ vcf-sort -t genome.dict new.vcf.gz > outnew.vcf&"
when i run
$ vcf-sort --help
it shows
Usage: vcf-sort > out.vcf
cat file.vcf | vcf-sort > out.vcf
Options:
-c, --chromosomal-order Use natural ordering (1,2,10,MT,X) rather then the default (1,10,2,MT,X). This requires
new version of the unix "sort" command which supports the --version-sort option.
-t, --temporary-directory Use a directory other than /tmp as the temporary directory for sorting.
-h, -?, --help This help message.
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