Kiran N' Bishwa
Kiran N' Bishwa
Has there been any update to accessing the `GT` values? I am still getting: print(variant.format('GT')) ['' '' '' '\x04\x04' '\x02\x02' '\x02\x02' '\x02\x02'] # this one is just too difficult to...
That `class` really is a nice representation. I think the method to mine the `genotype_bases` can also be added to it. I am writing a python tool to simplify the...
@brentp Any update on this issue ? Thanks,
It's because your VCF does not have the "PI" tag in FORMAT field. You may indicate any other equivalent tag or "CHROM" if you want the haplotype representation to be...
Hi @ConnieXuhm Please share your VCF file (both dosage and non-dosage) so I can tell if it can do what you want it to do. For a more controlled and...
@jamescasbon @martijnvermaat @ian1roberts @arq5x: Can some of you please give me some lead on this problem? Thanks,
@martijnvermaat @jamescasbon @alimanfoo @gitanoqevaporelmundoentero Not, sure why but I am still having a problem: c = record.samples[2] c.add_field('foo', 'bar') Traceback (most recent call last): File "/home/everestial007/PycharmProjects/stitcher/pHASE-Stitcher-Markov/markov_final_test/phase_to_vcf.py", line 111, in c.add_field('foo',...
@jamescasbon @martijnvermaat I have to add that there is no `add_field` method in the file `module.py`. https://github.com/jamescasbon/PyVCF/blob/master/vcf/model.py Any suggestions on how I can use `add_field` method???
I had similar issue, not sure if the exact one. You can access the name of samples right after reading the vcf file, rather then when trying to run the...
@jamescasbon @martijnvermaat @ian1roberts : Any update on this issue ?