Post date: Jan 23, 2015 7:45:13 PM
I am using samtools and bcftools to call variable sites for all 576 individuals combined:
cd /labs/evolution/data/callosobruchus/gbs/Assemblies/gbs2ref/
samtools mpileup -C 50 -d 50 -f cmacbbg9jan14gbs.fasta -q 10 -Q 15 -D -g -I *bam > cmacvariants.bcf
bcftools view -c -d 0.8 -g -p 0.01 -P full -t 0.001 -v cmacvariants.bcf > cmacvariants.vcf