Get BWA mapping stats (mapped, unmapped reads, number of reads with MAPQ20)

get_bwa_mapping_stats.sh

#! /bin/bash

echo -e "Samplename\tTotal_reads\tMapped_reads\tUnmapped_reads\tMAPQ20_reads\tPercent_mapped\tPercent_MAPQ20_reads"

for file in ./*bam
do
    filename=`basename $file`
    samplename=${filename%.bam}
    total_reads=`samtools view -c $file`
    mapped_reads=`samtools view -c -F 4 $file`
    unmapped_reads=`samtools view -c -f 4 $file`
    mapq_20=`samtools view -c -q 20 $file`
    percent_mapped=`bc <<< "scale = 3; ($mapped_reads/$total_reads)*100"`
    percent_mapq20=`bc <<< "scale = 3; ($mapq_20/$total_reads)*100"`     
    echo -e "$samplename\t$total_reads\t$mapped_reads\t$unmapped_reads\t$mapq_20\t$percent_mapped\t$percent_mapq20"

done