thiscodeWorks - Organizing the best of code online

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for file in *
do
file=${file//.bam/}
samtools sort -@ 14 $file.bam > $file.sorted.bam
samtools index -@ 14 -b $file.sorted.bam
samtools idxstats -@ 14 $file.sorted.bam > $file.idxstats.txt
done

samtools bam2counts

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