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Sorting may be done in 3 modes.
Sorting may be done in 3 modes.
Local: Your VCF file is mostly in order but not ordered in small stretches.
Local: Performs sorting within a local window. The window size may be set by the -w option. <br>
Chrom : Your VCF file is not ordered by the chromosomes in the header but is fully ordered within each chromosome.
Use this when your VCF records are grouped by chromosome but not ordered in short stretches.<br><br>
Full: Your VCF is unordered.
Chrom : 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>
Full: No assumptions made about the order. Records will be ordered by the order of contigs in the header. <br>
Smaller temporary ordered files are created and their names will be <output_vcf>.<no>.bcf and after generating <br>
these files, they are merged and output into <output_vcf><br>
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