first commit. script to subsample BAM files in a directory

dunnart/scripts/subsample.sh

+
+
+TRA=($(for file in B*_PPq30.sorted.dedup.bam; do echo $file |cut -d "_" -f 1-2;done))
+
+echo ${TRA[@]}
+
+for tr in ${TRA[@]};
+
+do
+
+echo ${tr}
+
+frac=$( samtools idxstats ${tr}_PPq30.sorted.dedup.bam | cut -f3 | awk 'BEGIN {total=0} {total += $1} END {frac=10000000/total; if (frac > 1) {print 1} else {print frac}}' )
+
+samtools view -bs $frac ${tr}_PPq30.sorted.dedup.bam > ../../results_10M/bowtie2/${tr}_PPq30.sorted.dedup.bam
+
+done