Post date: May 11, 2014 10:52:52 PM
I used samtools and bcftools to identify variant sites from the 473 whole genome sequences from the within generation experiment (note this means that I am missing 27 genomes?). The resulting bcf and vcf files will initially be in data/timema/timema_wgrs/assembliesExperiment/. Here are the commands I used:
cd /labs/evolution/data/timema/timema_wgr/assembliesExperiment/
samtools mpileup -P ILLUMINA -u -g -I -f ../../draft_genome/draft0.3/mod_lg_timemaGenome.fasta timemaTC*sorted.bam > tc_wgrs_variants.bcf
bcftools view -c -e -g -v -I -d 0.8 -p 0.001 -P full -t 0.001 tc_wgrs_variants.bcf