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=== Sorting ===
=== Sorting ===
Sorting may be done in 3 modes.
Local:
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>
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#sorts mills.bcf and outputs to standard out in a 1000bp window.
vt sort -m local mills.bcf
#sorts mills.bcf and locally sorts it in a 10000bp window and outputs to out.bcf
vt sort -m local -w 10000 mills.bcf -o out.bcf
#sorts an indexed mills.bcf with chromosomes not sorted in the contig order in the header
vt sort -m chrom mills.bcf -o out.bcf
#sorts a mills.bcf with no assumption
vt sort -m full mills.bcf -o out.bcf
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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
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=== Normalization ===
=== Normalization ===
