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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 

#use vcftools to get information about our variant set
vcftools --vcf raw_calls.vcf

#returns this:
		VCFtools - 0.1.15
		(C) Adam Auton and Anthony Marcketta 2009

		Parameters as interpreted:
			--vcf raw_calls.vcf

		After filtering, kept 3 out of 3 Individuals
		After filtering, kept 14117 out of a possible 14117 Sites

#now quality filter the raw calls
bcftools filter --exclude 'QUAL < 30' raw_calls.vcf | bcftools view -g ^miss > qced_calls.vcf

#check the new quality checked vcf
vcftools --vcf qced_calls.vcf