PyVCF
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jamescasbon
A Variant Call Format reader for Python.
when self.is_deletion is invoked for this type of record, a TypeError is thrown ``` -> if len(self.REF) > len(alt_allele): (Pdb) l 439 if self.is_indel: 440 # just one alt allele...
Could you please explain how the scripts in pyVCF/scripts work? (How to filter with those filters, how to make a new filter, anything really). Documentation and Docs@http://pyvcf.readthedocs.io/en/latest/API.html do not help....
Please see: http://nbviewer.ipython.org/4678244/ Advantages are the ability to do many fast numpy based operations, output to many different formats (hdf5, csv, excel). Requires we rewrite the parser quite extensively, ideally...
Hi all, Is there a wheels version for the PyVCF ? Is it possible to create a wheels for windows 64 bit. Thank you very much
I think this should be a requirement. I noticed the following differences from just reading in and writing out a vcf file: 1. header lines are in different order 2....
Hello, do you plan to support vcf 4.2? I'm getting the following error trying to read a MuTect2 vcf: ``` File "/illumina/thirdparty/python/python-2.7.5/lib/python2.7/site-packages/vcf/parser.py", line 159, in read_format "One of the FORMAT...
I introduced a bug when implementing the proper parsing of the FT annotation. I forgot to include code to correctly write the FT annotations. Right now, PyVCF produces an invalid...
The is currently no changelog for version 0.6.8. Since there have been some API changes, it would be nice if users migrating from 0.6.7 to 0.6.8 could anticipate those. Some...
Hi, when I try to install PyVCF 0.6.0 through python setup.py install on a mac I get the following: error: can't copy 'vcf/cparse.c': doesn't exist or not a regular file...
When the VCF Reader parses our VCF's header, there is a particular line that gets truncated. The line is added by GATK (sorry, the line is very long): `##GATKCommandLine.VariantFiltration=` Specifically,...
