I have a script to run samtools pileup for multiple files. The script worked if I ran one file at a time without loop, but it gave me error saying "Illegal variable name" with the loop. So, I think it is something wrong with the loop. I have to use the old version of samtools with the pileup for the downstream analysis. Please anyone help me out with the issue.
#! /bin/csh cd /share/gwascotton/GBS_data/pileup_trial/ source /usr/local/apps/samtools/samtools017a.csh for i in $(ls *.bam);do samtools pileup -c -l /share/gwascotton/GBS_data/merged_files.sorted.bam.pileup -f /share/gwascotton/GBS_data/Ghirsutum_458_v1.0.fa /share/gwascotton/GBS_data/pileup_trial/"$i" > /share/gwascotton/GBS_data/new/"$i".pileup done ;