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Illumina / Pisces

Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
GNU General Public License v3.0
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Creating a GenomeSize.xml for a soybean genome #69

Open brunabavelino opened 2 years ago

brunabavelino commented 2 years ago

Dear @tamsen We are having a bad time here trying to understand how to make a GenomeSize.xml for the soybean genome assembly 2 (https://data.jgi.doe.gov/refine-download/phytozome?organism=Gmax&expanded=275). Our intention is to use it for running the DNA Amplicom module of the Local Run Manager v3 for SNP calling. Is there any simple way to make this file? ;D Bruna

tamsen commented 2 years ago

Hi! Thanks for your interest in Pisces. Its so exciting to hear its involved in the soybean genome assembly! :)

1) Yes, you can use the CreateGenomeSizeFile executable to generate that file. See https://github.com/tamsen/Pisces/wiki/Pisces-Tools-5.3.0

2) You can get latest binaries here: https://github.com/tamsen/Pisces/releases/tag/v5.3.0.0

3) Can you please re-post your question here, https://github.com/tamsen/Pisces ? We are moving away from enterprise hosting.

Thanks! Tamsen

brunabavelino commented 2 years ago

Hi, thank you very much for your help. I will be checking the documentation and binary files. Of course, I will be reposting the question here. Best.

Bruna

brunabavelino commented 2 years ago

Hello, I would like to thank you again for your support and for your patience in helping me with the doubts I had regarding Pisces. I managed to do it thanks to your help. Thank you so much for your help and patience. Hugs. Bruna