PyVCF
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jamescasbon
A Variant Call Format reader for Python.
in vcf.model._Record._set_start_and_end, I notice that the first line initialized the affected start and end thus: self.affected_start = self.affected_end = self.POS and then after doing the start/end calculations in a zero-based...
Hoping to use PyVCF but a quick test suggested that file size would increase 50%. Given the gross size of these files nowadays (1T not unheard of), I would have...
I think it could be a good improvement to allow the PyVCF module to be able to add or update information fields in Call objects, that is, in the FORMAT...
Per the suggestion by @gotgenes in #161: > Note that for some reason the original author chose to indicate un-altered records by setting `_Record.ALT to [None]` (a list containing `None`)...
Id list
from the VCF spec: "ID - identifier: **Semi-colon separated list** of unique identifiers where available. If this is a dbSNP variant it is encouraged to use the rs number(s). No...
I'm still unbelievably angry that VCF even exists, when they could have used hdf5 or something. Anyway, I'm not convinced that hand rolled parsers are really where it's at in...
I've written a simple in-memory VCF sorting script that uses PyVCF to sort one or more files into a particular chromosome ordering. Since this is a prerequisite for utils.walk_together(..), I...
`vcf.model.nucl_diversity` calculates `num_chroms = float(2.0 * self.num_called)`. This is not accurate for non-diploid sites, such as sex chromosome sites.
Hi, thanks for putting together such a wonderful library. Could you please take a look into this issue?. From [VCF spec](http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41): > POS position: The reference position, with the 1st...
