PyVCF
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jamescasbon
A Variant Call Format reader for Python.
Hello, I need to extract the 'AD' field from VCF file, but I couldn't locate the object for the AD field: "Allelic depths for the ref and alt alleles in...
I have a vcf full of SVs, and I want to read them in as class vcf.model._Breakend instead of vcf.model._Record. Then I can easily query their connectingSequence and other variables....
`0.6.8` was released in 2016, perhaps time for a new release? There have been several bug fixes that would be great to see in a new release. Please let me...
The vcf 4.3 version introduced a new method of representing a `deletion spanning variant` by `*`. We obviously don't want `gt_bases` output as A/* or as `*/*` but the real...
This allows for nice things like type annotations for functions that accept a `Record` as well as users building dummy `Record` objects for testing. For example I can now do...
I am using this package to extract certain records from the original vcf file. Recently I extracted synonymous sites and nonsynonymous sites from multiple vcf files. The code I was...
[failcase.vcf.gz](https://github.com/jamescasbon/PyVCF/files/1282898/failcase.vcf.gz) attached is a test case I've found in the wild. I've trimmed this down to a single line, which fails in that call.data has no .GT can anyone explain...
I have been playing around with pyVCF and found I was able to read in bcf files by adding the following lines to the reader object: ``` if fsock: self._reader...
``` file = "some_file.vcf" vcf_reader = vcf.Reader(open(file, 'r')) for record in vcf_reader: print(record) for record in vcf_reader: print(record) ``` The second for loop doesn't print anything as vcf_reader is empty....
dear all: when I filter file by vcf file,I have a problem,when I use vcf module in loop，after I use i.CHROM,next loop,it doesn't work，I must enter myvcf = vcf.Reader(open(file,'r')) again,...
