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#start and idev session if you haven't
idev
#copy over the exercise directory
cds
cd rad_intro/
cp -r /work/02260/grovesd/lonestar/intro_to_rad_2017/genotyping/ddRAD_mpileup .
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 |
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