Changes

Sorting may be done in 3 modes.

Sorting may be done in 3 modes.

Local:  

Local: Your VCF file is mostly in order but not ordered in small stretches.

 

Chrom : Your VCF file is not ordered by the chromosomes in the header but is fully ordered within each chromosome.

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.

Full: Your VCF is unordered.

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