A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Dear all, is it possible to use sarek for plants ? the idea is also to get a joint vcf for all genotypes

<@U07527LNWHW> is using it for tomatoes if I remember well

<@U03D997D0LV> can you be so kind to share the code you're using ? thanks!

I'm on vacation, can you please remind me on Tuesday?

Here is the relevant part of the params file:
```tools: freebayes,strelka,tiddit,cnvkit
skip_tools: baserecalibrator

igenomes_ignore: true
fasta: /path/to/genome.fna

normalize_vcfs: true
snv_consensus_calling: true
consensus_min_count: 2```
Some relevant considerations:
• Base recalibration is not available unless you have a known SNP file
• You probably need to download the reference genome, as igenomes has a very limited selection of plants
• All variant callers should work normally, assuming sufficient sequencing data quality
• I have not been able to set up either of the "nice" annotation tools, since databases are not well standardized for plants; you might have to annotate outside sarek
For the VCF, you will get the standard output of the tools, plus a consensus VCF if requested. It should work fine if your plants are diploid, or at least behave like they are. I am not sure what will happen if that is not the case.