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I am trying to run the popsize module. However, I didn't create my vcf files with snpArcher, which is becoming quite challenging. I am running the software, and I get the following error: No rule to p…
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### Description of feature
I have data consisting of several unrelated trios and several individuals. Is it possible to run the pipeline with just one samplesheet (where cases have different case_id)…
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Hello,
I am experiencing an issue while running the SvAnna CLI tool. I receive the following error message when executing the command:
ERROR o.m.svanna.cli.cmd.PrioritizeCommand - Error: Error rea…
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### Description of the issue
When reading bgzip-compressed data from a stream (e.g. over the network or from a pipe), htsjdk can stop early and not read the stream all the way to the end, processin…
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Hello, I got the following error when converting data formats.
command line:
vcf_to_ima.py --vcfs chr01_4gt/chr01_4gt_Chr01-797055-798759.vcf chr01_4gt/chr01_4gt_Chr01-819732-821385.vcf chr01_4gt/ch…
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Firstly thx for your amazing work.
I really like the concept behind your tool :)
Now concerning the bug:
I worked with a fresh Colab notebook
* MMSplice version:
Installation with pip: `mmspl…
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Hello,
I successfully ran est_p, and am now trying to estimate the hybrid index using default settings. The data for the putative hybrids is formatted the same way as the parentals, but I am gettin…
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Hi,
I'm trying to annotate a VCF with only 248 variants using the gnomad genomes VCF as annotation and it takes about 2 hours to run. Both the input VCF and the annotation VCF are indexed with tab…
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Hello,
I am attempting to run the following command on the corBra data in the test-data folder.
`python /home/boltonp/miniconda3/envs/degenotate/bin/degenotate.py -a corBra.gff.gz -g corBra.fa.…
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The function currently loads the raw data, but doesn't process it. Check the code in `greedyPopMix()` and the original MATLAB code to see what else needs to be done (e.g. call `handleData()`).
To clo…