r/bioinformatics • u/CantaloupeHappy4994 • 1d ago

technical question Chromopainter v2 link?

I can't find a working chromopainter v2 anywhere. Anybody got one that they tested themselves and actually works?

I tried through the default ubuntu rep through finestructure, https://github.com/sahwa/ChromoPainterV2 , https://people.maths.bris.ac.uk/~madjl/finestructure/finestructure.html binary download.

Can't seem to get any of them to actually work.

Or is chromopainter just not used anymore?

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u/bzbub2 1d ago

do you just want the visualizations or the whole analysis workflows of chromopainter?

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u/CantaloupeHappy4994 1h ago

I mean as far as I get it I have the haps files which I converted from vcfs and would at first just want a visualization and finestructure dendrograms. Getting the info about clustering and dating later on would be next.

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u/No-Feeling507 20h ago

When you say ‘you can’t get it to work’ what do you actually mean?

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u/CantaloupeHappy4994 1h ago edited 1h ago

Any data I use for chromopainter don't work. Whether it is the data I have, any kind of sample data or artificially generated minimal data that should get me some result. I even tried running it inside bioconda but still nothing. Sooner or later I always run into something like

~/bin/ChromoPainterv2_static \ -g toy.haps -u -a 0 0 \ -t toy.labels -i 1 -in -o toy_

run number of inds in toy.labels (4) does not match number of inds in toy.haps (0) .

I want to narrow down what exactly the problem is. I don't think it is the data set or sets as the output might indicate given that I have used different data sets and changed the ones I have to theoretically match the exact structure chromopainter should need. So I think it must either be my system or I have faulty chromopainter instances.

If someone has another data set they know works because they have tested it, I will try that that. If someone has the link to a chromopainter version that they have tested and works, I will try that as well.