Compress/index input with bgzip+tabix

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GP files (both intervals and single position files) can be compressed+indexed with tabix. PileLine now supports this format as input for its commands.

NOTE: PileLine will recognize a input file as compressed if they have the .bgz extension.

Compressing GP files with tabix

  1. Download tabix software from: http://samtools.sourceforge.net/tabix.shtml
  2. Compress a file (for example a .bed)
cat myfile.bed | bgzip > myfile.bed.bgz
tabix -p bed myfile.bed.bgz
#tabix has now created the myfile.bed.bgz.tbi, which is the index.
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