sorted bam file
Hi,
I am trying to calculate the sequencing depth for sorted bam files made using bowtie. I am using:
samtools depth bowtie_sorted.bam | awk '{sum+=$3} END { print "Average = ",sum/NR}'
I have many sorted bam files and I want to calculate the depth for all using one array job rather than calculating for all files individually. Can anyone help writing such an array? Thanks!
1 answer
ls *.bam | parallel -j <NumberOfParallelJobs> "samtools flagstat {} > {.}.flagstat"
This gives a complete overview over the number of mapped/unmapped reads etc.
Alternatively, index the files and use samtools idxstats followed by summing up the reads of all chromosomes.
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