depth calculation for targeted resequencing

Question

[genesneuro]

hi I am new to NGS. In a targeted re sequencing experiment using molecular inversion probes. how can we calculate the Target coverage (depth in X). How is it different from exome depth calculations

[genesneuro]

Thank you for reply. So if the output of depth calculations shows like this at each site (for 10 bases) 289,581,581,581,581,581,581,581,581, 581 is my depth of coverage for the interval = interval read depth/10 X, (in this case 551.8X) ?

[Devon Ryan]

Correct. BTW, samtools depth defaults to not printing positions with 0 coverage. I think there's a flag to get around that (-aa or something like that), but keep that in mind if you need to calculate a bunch of regions in an automated fashion.

[Jorge Amigo]

Devon is right mentioning that, because if you're willing to get the average depth then you have to consider 0 coverage regions too. you may want to have a look to bedtools' genomecov to continue learning about extracting depth of coverage information, or to picard's CollectHsMetrics which calculates directly the mean target coverage.

Answer 1

[Jorge Amigo]

the concept depth of coverage, being the number of reads at each particular position of the genome, is independent of the experiment you run. if you have aligned reads in a bam file you can extract the depth of coverage or read depth in many different ways already discussed in Biostarts. my favourite one is samtools depth -b target.bed file.bam, as it's one of the fastest methods although it's limited to 8000x.

Answer 2

[svp]

As an update you can use

To get the mean depth of coverage

bedtools coverage -a $bedfile-b $bamfile -mean > mean.bedgraph

output the per base read depth for each region in the BED file using bedtools

bedtools coverage -a $bedfile -b $bamfile -d > per.base.depth.bedgraph

calculate coverage at each position in a bed file using samtools depth

samtools depth -b $bedfile -aa $bamfile > $bamfile.depth.txt