Yleaf
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genid
Yleaf software for human Y-chromosomal haplogroup inference from next generation sequencing data
Hello! Would it be possible to add T2T to Yleaf positions and support for T2T-CHM13v2.0 reference? Thanks!
Are there plans to add Yleaf to PyPI and/or bioconda? (I did not find it on either. Sorry if it is already there.) The existing conda environment file is already...
Dear developer: The species we are engaged in is pig, a very good medical model animal. But we have noticed that this software is designed for humans, I would like...
# Add command-line options for custom reference genomes ## Changes This PR adds the ability to specify custom reference genome files directly via command-line options, making Yleaf more flexible and...
Hello the Yleaf manual linked on the main github page doesn't explain the --ancient_DNA argument, would be helpful to update that.
This program make the invalid assumption that mutated global variables (like `BACKBONE_GROUPS`) will have up-to-values in child proceses. This is very much not true, an explicitly stated by the Python...
I get this error when running for the first time. It looks like the program does not correctly handle the case that the reference genome does not exist. ``` INFO...
In the get_frequencies() function the deletions and insertions are likely improperly handled. Please read the [mpileup specification](https://www.htslib.org/doc/1.14/samtools-mpileup.html). In one hand the -NUM+SEQ and the +NUM+SEQ notation only used at the...
This is a very minor issue which usually cause no differences, however it hinders comparability on large data sets. The problem only affects CRAM files, as the mpileup in this...
Hi Hope you're well! Are the install instructions out of date? How does one get Yleaf running? From: [https://github.com/genid/Yleaf](url) > The easiest way to get Yleaf up and running is...
