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
samtools depth can use a bedfile
Thank you so much, I will try this!
Hi ATpoint, do you know what the variable $3 is? Thanks! Amy
What do you mean? The third column in the depth output (that is what
$3
) means is what we want to sum up. Does that make sense?Hi, yes you are right, I'm sorry! Slurm was messing with the command! Thanks for all your help