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=== Sorting ===
=== Sorting ===
Sorting may be done in 3 modes.
Sorting may be done in 3 approaches.
Locally:<br>
Performs sorting within a local window. The window size may be set by the -w option. The default window size <br>
is 1000bp and if a record is detected to be potentially out of order due to a small window size, it wil be reported.<br>
Use this when your VCF records are grouped by chromosome but not ordered in short stretches.<br><br>
Use this when your VCF records are grouped by chromosome but not ordered in short stretches.<br><br>
By chromosome: <br>
Your VCF file is not ordered by the chromosomes in the header but is fully ordered within each chromosome.<br>
The VCF file should be indexed and vt will output the records in the order of chromosomes given in the header. <br> <br>
The VCF file should be indexed and vt will output the records in the order of chromosomes given in the header. <br> <br>
Full: No assumptions made about the order. Records will be ordered by the order of contigs in the header. <br>
Full sort [default option]: <br>
Smaller temporary ordered files are created and their names will be <output_vcf>.<no>.bcf and after generating <br>
No assumptions are made about the VCF file. Records will be ordered by the order of contigs in the header. <br>
these files, they are merged and output into <output_vcf><br>
Smaller temporary ordered files are created and their names are <output_vcf>.<no>.bcf and after generating <br>
these files, they are merged and output into <output_vcf>.<br>
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<div class=" mw-collapsible mw-collapsed">
vt sort -m chrom mills.bcf -o out.bcf
vt sort -m chrom mills.bcf -o out.bcf
#sorts a mills.bcf with no assumption
#sorts a mills.bcf with no assumption
vt sort -m full mills.bcf -o out.bcf
vt sort mills.bcf -o out.bcf
<div class="mw-collapsible-content">
<div class="mw-collapsible-content">
usage : vt sort [options] <in.vcf>
usage : vt sort [options] <in.vcf>
options : -m sorting modes [full]
options : -m sorting modes. [full]
local : locally sort within a window.
local : locally sort within a 1000bp window. Window size may be set by -w.
chrom : sort chromosomes based on order of contigs in header.
chrom : sort chromosomes based on order of contigs in header.
input must be an indexed vcf.gz
input must be indexed.
full : full sort with no assumptions
full : full sort with no assumptions.
-o output VCF/VCF.GZ/BCF file [-]
-o output VCF/VCF.GZ/BCF file. [-]
-w local sorting window size [0]
-w local sorting window size, set by default to 1000 under local mode. [0]
-p print options and summary []
-p print options and summary. []
-? displays help
-? displays help
