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sanjaynagi / rna-seq-pop

Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data
https://sanjaynagi.github.io/rna-seq-pop/
MIT License
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freebayes add parameter: min-alternate-fraction 0.05 #103

Closed sanjaynagi closed 1 month ago

sanjaynagi commented 1 month ago

Add new freebayes parameter which was by default set to 0.20.

In theory this means that previously, if 10% of the reads in a sample are alternate, it will not be called as a SNP. This is fine for diploid samples, but not for high ploidy, which is how we approach pooled samples.