PyVCF
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jamescasbon
A Variant Call Format reader for Python.
File "/opt/anaconda/anaconda3/bin_vcf_melt", line 16, in inp = file(sys.argv[1]) Does file need to be replaced with open here? I ran this command as: vcf_melt my_vcf_file.vcf and I get the error above....
I ran into the following problem using the latest pyvcf from pip. I should note that this is for the following haploid record. ``` #CHROM POS ID REF ALT QUAL...
When working with PyVCF, I realized that there was a strange issue with the .ALT attribute of a record. It seems to me that it just returns lists that contain...
Added the method `add_field`. Taken from https://github.com/jamescasbon/PyVCF/blob/wip/82-add-call-data/vcf/model.py
Hi, apologies for submitting a question as an issue. I wasn't quite sure where to ask it (I couldn't find a mailing list, so please point me to it if...
Can some one give me a some heads up on how to approach this problem? I read the vcf file and generated the following information (in text file). Now, I...
Here is what I am doing: I'm working with a very large vcf file (816 samples). Our experiment has included duplicate samples to try and pick out false positives. The...
I've added support for bcf files by using bcftools. Supports fetching specific regions and iteration. Includes checking that indices exist, and that bcftools is available.
Currently _Contig is defined as _Contig = collections.namedtuple('Contig', ['id', 'length']) There are other common k:v pairs in the ##contig lines. For example, the VCF 4.1 specs give the following examples...
See Issue #153 which was closed by the reporter after a developer suggested that existing behavior (which is to return an empty list for FILTER, when the filter column contains...