Scripts for variant calling from resequencing data on peach accessions (Prunus persica)
- make sample sheet for IGA samples: R script
make_samplesheet.r - make sample sheet for BGI samples: Python script
make_sample_sheet.py(to be completed: include the case of multiple files within subfolders --> more than two files per samples, multiple R1/R2 fastq files)
Bash scripts to use bcftools and vcftools to subset the vcf file from variant calling and to produce summary statistics
- normalise_vcf.sh: sometimes Freebayes adds the whole haplotype around a SNP --> need to remove the non-polymorphic sites and leave only yhe SNP
- snp_only_from_vcf.sh: take only biallelic SNPs (remove MNPs/Indels, triallelic sites)
- stats: frequency, missing rate
- quality filter: how?
- merge?
- approaches with BGLR from https://github.com/gdlc/BGLR-R/blob/master/inst/md/GxE_usingInteractions.md (paper: https://pubmed.ncbi.nlm.nih.gov/25660166/)
- thin: parameter that tells BGLR every how many iterations results are to be saved to external files
- other ...
- other approaches ...