Post date: Feb 25, 2014 5:40:59 PM
I merged the new and old family alignments, and the merged alignments are in data/timema/timema_mappingfams/merged*/. Here is an example for a single individual:
cd /home/A01963476/data/timema/timema_mappingfams/
samtools merge -n -h /home/A01963476/data/timema/timema_mappingfams/fam25270by25271/aln25300.sorted.bam /home/A01963476/data/timema/timema_mappingfams/mergedFam25270x25271/alnMAP25300.merged.bam /home/A01963476/data/timema/timema_mappingfams/fam25270by25271/aln25300.sorted.bam /home/A01963476/data/timema/timema_mappingfams/NCGR/alignments/alnMAP25300.sorted.bam
samtools sort /home/A01963476/data/timema/timema_mappingfams/mergedFam25270x25271/alnMAP25300.merged.bam /home/A01963476/data/timema/timema_mappingfams/mergedFam25270x25271/alnMAP25300.merged.sorted
samtools index /home/A01963476/data/timema/timema_mappingfams/mergedFam25270x25271/alnMAP25300.merged.sorted.bam
I using samtools for variant calling in each family, e.g.,
cd /home/A01963476/data/timema/timema_mappingfams/mergedFam25270x25271/
samtools mpileup -f /home/A01963476/data/timema/draft_genome/draft0.1/timemaGenome.fasta -q 20 -Q 20 -D -g -u -I *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