Skip to content


Subversion checkout URL

You can clone with
Download ZIP
Fetching contributors…

Cannot retrieve contributors at this time

145 lines (104 sloc) 3.831 kB


Please use the PyVCF repository. Pull requests gladly accepted. Issues should be reported at the github issue tracker.

Running tests

Please check the tests by running them with:

python test

New features should have test code sent with them.


0.6.0 Release

  • Backwards incompatible change: is now a namedtuple (previously it was a dict)
  • Optional cython version, much improved performance.
  • Improvements to writer (thanks @cmclean)
  • Improvements to inheritance of classes (thanks @lennax)

0.5.0 Release

VCF 4.1 support:
  • support missing genotype #28 (thanks @martijnvermaat)
  • parseALT for svs #42, #48 (thanks @dzerbino)
  • trim_common_suffix method #22 (thanks @martijnvermaat)
  • Multiple metadata with the same key is stored (#52)
Writer improvements
  • A/G in Number INFO fields #53 (thanks @lennax)
  • Better output #55 (thanks @cmclean)
  • Allow malformed INFO fields #49 (thanks @ilyaminkin)
  • Added bayes factor error bias VCF filter
  • Added docs on vcf_melt
  • filters from @libor-m (SNP only, depth per sample, avg depth per sample)
  • change to the filter API, use docstring for filter description

0.4.6 Release

  • Performance improvements (#47)
  • Preserve order of INFO column (#46)

0.4.5 Release

  • Support exponent syntax qual values (#43, #44) (thanks @martijnvermaat)
  • Preserve order of header lines (#45)

0.4.4 Release

  • Support whitespace in sample names
  • SV work (thanks @arq5x)
  • Python 3 support via 2to3 (thanks @marcelm)
  • Improved filtering script, capable of importing local files

0.4.3 Release

  • Single floats in Reader._sample_parser not being converted to float #35
  • Handle String INFO values when Number=1 in header #34

0.4.2 Release

  • Installation problems

0.4.1 Release

  • Installation problems

0.4.0 Release

  • Package structure
  • add vcf.utils module with walk_together method
  • samtools tests
  • support Freebayes' non standard '.' for no call
  • fix vcf_melt
  • support monomorphic sites, add is_monomorphic method, handle null QUALs
  • filter support for files with monomorphic calls
  • Values declared as single are no-longer returned in lists
  • several performance improvements

0.3.0 Release

  • Fix for python < 2.7
  • Add __eq__ to _Record and _Call
  • Add is_het and is_variant to _Call
  • Drop aggressive parse mode: we're always aggressive.
  • Add tabix fetch for single calls, fix one->zero based indexing
  • add prepend_chr mode for Reader to add chr to CHROM attributes

0.2.2 Release

Documentation release

0.2.1 Release

  • Add shebang to

0.2 Release

  • Replace genotype dictionary with a Call object
  • Methods on Record and Call (thanks @arq5x)
  • Shortcut parse_sample when genotype is None

0.1 Release

  • Added test code
  • Added Writer class
  • Allow negative number in INFO and FORMAT fields (thanks @martijnvermaat)
  • Prefer vcf.Reader to vcf.VCFReader
  • Support compressed files with guessing where filename is available on fsock
  • Allow opening by filename as well as filesocket
  • Support fetching rows for tabixed indexed files
  • Performance improvements (see test/
  • Added extensible filter script (see,


Project started by @jdoughertyii and taken over by @jamescasbon on 12th January 2011. Contributions from @arq5x, @brentp, @martijnvermaat, @ian1roberts, @marcelm.

This project was supported by Population Genetics.

Jump to Line
Something went wrong with that request. Please try again.