Post date: Feb 27, 2014 4:47:58 PM
My initial variant calling attempt did not grab the correct files, so I ran it again. I also tweaked the quality thresholds (less stringent than the last attempt, but more so than the original analysis with the data from the first batch of seqeuncing). Here are the new commands (note the inclusion of sorted in the glob):
cd /home/A01963476/data/timema/timema_mappingfams/mergedFam25270x25271/
samtools mpileup -f /home/A01963476/data/timema/draft_genome/draft0.1/timemaGenome.fasta -q 10 -Q 15 -D -g -u -I *sorted.bam > fam25270x25271.bcf
bcftools view -c -e -g -v -I -d 0.8 -p 0.001 -P full -t 0.001 fam25270x25271.bcf > fam25270x25271.vcf