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cggh / scikit-allel

A Python package for exploring and analysing genetic variation data
MIT License
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FORMAT #331

Open javadnoorb opened 4 years ago

javadnoorb commented 4 years ago

Hi,

I have encountered the following issue that I wanted to let you know of.

When I use the following command:

df = allel.vcf_to_dataframe('myfile.vcf', fields=['calldata/*', 'variants/*'])

The FORMAT field is not parsed. However it is parsed when I use:

callset = allel.read_vcf('myfile.vcf', fields=['calldata/*', 'variants/*'])
alimanfoo commented 4 years ago

Hi @javadnoorb, yes this is by design, the current implementation of vcf_to_dataframe ignores the FORMAT fields. There is some work in #252 but that is stalled I'm afraid as I haven't had time to review.

kyaki commented 1 year ago

HI, I see this ticket is a few years old now but is still open, was wondering if this work has been dropped? I am still running into this issue. Perhaps there is some new way to parse vcfs into dfs that I have not found yet?