change freebayes min depth param

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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change freebayes min depth param #42

Open sanjaynagi opened 2 years ago

sanjaynagi commented 2 years ago

This needs changing to 4 ideally as previous studies shown variant calling accurate above this level. already we have missingness filters high so this probably wont make much difference.

sanjaynagi commented 2 years ago

Related -

Should we have a filter for:

Sites of poor mapping quality?
Sites at homopolymers
Sites at exon-intron junctions

and how many SNPs will this remove?

sanjaynagi commented 2 years ago

We should also potentially use a maximum depth filter within freebayes, we have --use-best-n-alleles which may do the same job, however.