Changes

=== Concatenate ===

=== Concatenate ===

Concatenate VCF files.  Assumes individuals are in the same order and files share the same header.

Concatenates VCF files.  Assumes individuals are in the same order and files share the same header.

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   #concatenate chr1.mills.bcf and chr2.mills.bcf

   #concatenates chr1.mills.bcf and chr2.mills.bcf

   vt cat chr1.mills.bcf chr2.mills.bcf -o mills.bcf

   vt cat chr1.mills.bcf chr2.mills.bcf -o mills.bcf

   #concatenate chr1.mills.bcf and chr2.mills.bcf with the naive option

   #concatenates chr1.mills.bcf and chr2.mills.bcf with the naive option.

   #naive option assumes the headers are all the same and avoids translation of

   #The naive option assumes that the headers are all the same and skips

   #encodings between BCF files that have different headers. This is a much faster

   #merging headers and translating encodings between BCF files.   This is  

  #option if you know the nature of your BCF files in advance.

  #a much faster option if you know the nature of your BCF files in advance.

   vt cat -n chr1.mills.bcf chr2.mills.bcf -o mills.bcf

   vt cat -n chr1.mills.bcf chr2.mills.bcf -o mills.bcf