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You will want to locally sort a VCF file if you are aware that the records are not in order in short stretches. This will not work if the records are not in chromosomal order. The window dictates the size of the region to buffer the records while sorting.
You will want to locally sort a VCF file if you are aware that the records are not in order in short stretches. This will not work if the records are not in chromosomal order. The window dictates the size of the region to buffer the records while sorting.
usage : vt sort [options] <in.vcf>
options : -m sorting modes [full]
local : locally sort within a window.
chrom : sort chromosomes based on order of contigs in header.
input must be an indexed vcf.gz
full : full sort with no assumptions
-o output VCF/VCF.GZ/BCF file [-]
under fill sorting mode, this is a prefix
-w local sorting window size [0]
-p print options and summary []
-? displays help
=== Normalization ===
=== Normalization ===
