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LAST UPDATED: 24 Oct, 2022 
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DESCRIPTION. Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates an index file ( in.tab.bgz.tbi or in.tab.bgz.csi ) when region is absent from the command-line. The input data file must be position sorted and compressed by bgzip which has a gzip (1) like interface. After indexing, tabix is able to quickly retrieve data
https://www.htslib.org/doc/tabix.htmlCompress/index input with bgzip +tabix. From PileLine. Jump to: navigation, search. 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.
https://www.sing-group.org/pileline/index.php/Compress/index_input_with_bgzip%2BtabixHowever, if your compressed .bz2 file does not contain multiple pieces, then there will be no speed advantage by decompressing in parallel. Since the standard tools generally only create one piece in the compressed file, most files will have no speed advantage when decompressing using mpibzip2.
https://rc.byu.edu/wiki/index.php?page=Parallel+BZIP2+CompressionLack of support for gzipped vcf files not compressed with bgzip ¶ Normal gzipped files do not allow for random or indexed access to the information contained on them, only files compressed with bgzip are indexable. As such, the Sentieon® software does not support gzipped VCF files as ...
https://support.sentieon.com/manual/appendix/troubleshooting/Bgzip compresses files in a similar manner to, and compatible with, gzip (1). The file is compressed into a series of small (less than 64K) 'BGZF' blocks. This allows indexes to be built against the compressed file and used to retrieve portions of the data without having to decompress the entire file.
The [email protected] tells bgzip to use four threads. You can increase this if your machine has more cores. The last line directs the block-gzip compressed output to a file called file.vcf.bgz. On my MacBook Pro this process took one minute to re-compress a 214MB file.
Any file larger than that will not be compressed using the Gzip algorithm. That is, however, relying on the older algorithms. Newer versions of Gzip work with larger files, though it can often take a bit of time to compress them and uncompress them.
42 The magic numberfor gzip compressed files is 1f 8b. Although testing for this is not 100% reliable, it is highly unlikely that "ordinary text files" start with those two bytes—in UTF-8 it's not even legal. Usually gzip compressed files sport the suffix .gzthough.
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