Nextflow and python scripts acompanying the paper: Deleterious mutations and the role of rare genetic variation on rice gene expression
Nextflow scripts - SNP and indel calling: calling.config calling.nf process.conf process.nf
Processing and merging SVs:
gridss_sample_processing.py
- input a vcf file of BND variants, the output of SV callers such as GRIDSS
- parses BND into duplications, deletion, insertions and copy number variable regions (complex rearrangement regions, where breakend intervals overlap within the sample)
- this script uses functions from 'write_vcf.py', 'cnvr_functions.py'
run_duphold.sh:
- use duphold to annotate SVs in VCFs per sample (https://github.com/brentp/duphold/)
- bam files for each sample are required
merge_samples.py
- merges SVs VCFs of individuals to group, this is preformed after duphold filtering
- this script uses functions from 'write_merged.pys'