SNP calling samtools pipeline that forms part of a larger project to compare various SNP calling algorithms that was published in Molecular Ecology Resources: https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13628
Haploid megagametophyte sequencing data from 106 Lodgepole pine progeny Diploid data from mother of the 106 progeny
Compare efficieny of SNPs called from SAMtools, GATK, varscan and FreeBayes This is only the samtools (bcftools) part
all analyses were run the Graham server of compute canada slurm submisison manager was used
bcftools (samtools) was used to call SNPs and vcftools was used to filter SNPs with basic filters, more stringent filters can be also implemented as required
NB: samtools mpileup to call SNPs is deprecated, thus we use bcftools mpileup
NB: samtools mpileup is still fine to direct to tools like varscan etc
NB: be careful with the new -G population flag in bcftools
sbatch script contains all the steps