Question: Recommendations For Python Vcf Parser/Writer?
11
gravatar for Reece
8.1 years ago by
Reece270
United States
Reece270 wrote:

I'm looking for a VCF 4.1 parser and writer. I'm aware of these:

Do you know of other options or have recommendations to share?

vcf python variation variant • 13k views
ADD COMMENTlink modified 10 weeks ago by Dataman310 • written 8.1 years ago by Reece270
14
gravatar for brentp
8.1 years ago by
brentp23k
Salt Lake City, UT
brentp23k wrote:

I've looked at the ones you mention and any others I could find. This one seems to be the most complete and easiest to use: https://github.com/jdoughertyii/PyVCF

usage is like:

for rec in VCFReader(open('some.vcf')):
    print rec.CHROM, rec.POS, rec.filter, rec.info["AF"]

though, it does not have a writer class.

EDIT:

This, has become the official fork and it has a writer class.

ADD COMMENTlink modified 8.0 years ago • written 8.1 years ago by brentp23k
1

I am using that library as well (with a couple of minor mods) for another project. Works okay for me.

ADD REPLYlink written 8.1 years ago by Aaronquinlan11k
1

The idea for the UPPER was to distinguish native (upper) fields from derived (lower) attributes/methods. For better or worse...

ADD REPLYlink written 8.0 years ago by Aaronquinlan11k

thanks. any idea why UPPERCASE field names?

ADD REPLYlink written 8.0 years ago by Haibao Tang3.0k

Not sure other than that's how they appear in the VCF filter. You could file a bug at https://github.com/jamescasbon/PyVCF

ADD REPLYlink written 8.0 years ago by brentp23k

Pyvcf is too slow ... Is there anything else in python using C++ as backend ?

ADD REPLYlink written 3.5 years ago by sacha1.8k

CyVCF2 https://github.com/brentp/cyvcf2

ADD REPLYlink written 2.0 years ago by Eli Korvigo160
2
gravatar for Erik Garrison
8.0 years ago by
Erik Garrison2.2k
Napoli, IT / UCSC
Erik Garrison2.2k wrote:

For C++, I've written vcflib. It has utilities for a number of functions, such as haplotype-based file comparisons (for accurate indel comparisons), filtering, and statistical summarization. It can operate on uncompressed or compressed and tabix indexed VCF files. Mostly, I've used it as a reader/writer class for other projects.

ADD COMMENTlink written 8.0 years ago by Erik Garrison2.2k
0
gravatar for Dataman
10 weeks ago by
Dataman310
Finland
Dataman310 wrote:

I know this question is rather old and has an answer but it is still a relevant question. A recent, alternative for parsing VCF files in Python (both versions 2 and 3) is cyvcf2 which is made by two well known bioinformaticians: Brent Pedersen and Aaron Quinlan.
GitHub link: http://brentp.github.io/cyvcf2/ and https://github.com/brentp/cyvcf2.
The Journal article: https://academic.oup.com/bioinformatics/article/33/12/1867/2971439

ADD COMMENTlink written 10 weeks ago by Dataman310
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