run mpileup
#start and idev session if you haven't idev #copy over the exercise directory cds cd rad_intro/ cd ddRAD_mpileup/ #index the reference for samtools module load samtools samtools faidx stickleback_chrom3.fasta #make a list of the bam files ls *.bam > my_bamfiles.txt #run mpileup samtools mpileup -f stickleback_chrom3.fasta -t DP,AD,ADF,ADR,SP -u -b my_bamfiles.txt > mpileup_results.bcf #now call genotypes from the mpileup results bcftools call -vmO v -o raw_calls.vcf mpileup_results.bcf