Hello,
I know that there are lots of coverage questions on here but quite a few are 10 years + and really confusing.
I have WES fastq files, I have mapped these to hg38 and have their bam files. I also have the bed files for the Exome panel used in the sequencing.
I wish to work out the coverage (like 100X). I know that bedtools has a way but I am finding it hard to work out.
Do I need to get a list of the gene locations even though I have the exon region bed files?
Thanks! Amy
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hello_bioinf •
Adapting from Tools To Calculate Average Coverage For A Bam File?:
samtools view -u -L exome.bed your.bam \
| samtools depth -a \
| awk '{sum+=$3} END { print "Average = ",sum/NR}'
The first one subsets for alignment covering the exome (use the bed file with the targets of the capture), and the rest then calculated the average coverage.
samtools depth can use a bedfile
samtools depth -b exome.bed -a in.bam | awk '{sum+=$3} END { print "Average = ",sum/NR}'
Thank you so much, I will try this!
Hi ATpoint, do you know what the variable $3 is? Thanks! Amy
Hi, yes you are right, I'm sorry! Slurm was messing with the command! Thanks for all your help
https://github.com/brentp/mosdepth
mosdepth -by exome.bed --no-per-base output in.bam
look into the summary Total region to get the mean depth
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