Determining Each Samples Coverage Area

Question

[Robert Sicko]

First time I am working with NGS data. I've got a BAM file with mapped reads for my samples and a BED file with the regions in HG19 that were targeted (used an Ion-torrent ampliseq panel). Are there any tools that can output something similar to this:

**Sample      Amplicon           Chromosome           Start_coordinate_of_coverage             End_coordinate_of_coverage**
Sample1       amp_001                chr6                 1,000,000                                   1,000,250
Sample2       amp_001                chr6                 1,000,111                                   1,000,255
Sample1       amp_002                chr6                 1,000,200                                   1,000,333

I basically want to know for each gene what coverage we have for each sample.

EDIT: changed column headings, I'm looking for coordinates that have coverage, not depth at each exon.

[Pierre Lindenbaum]

duplicate of Calculate per exon/per gene coverage

[Robert Sicko]

Sorry I missed that post in my search... I actually did come across your variation toolkit in another post too. Can I run beddepth on a BAM that contains all of my samples or should I first split the bam by sample and then run beddepth? I guess I would have to split the BAM and run on each sample individually if I wanted the start and end of coverage for each sample anyway right?

Thanks!

[Pierre Lindenbaum]

you should use the GATK-depth of coverage solution.

[Robert Sicko]

Hey Pierre, I'm finally getting back to this... After reading through the information about GATK's depthofcoverage walker, I don't think this is what I am looking for. I don't want to output depth at each exon, I want coordinates for regions that have reads mapped to them from a targeted BED file.

[Pierre Lindenbaum]

then just see

extract alignment from very large BAM file

[Jorge Amigo]

I would rather go for Tools To Calculate Average Coverage For A Bam File?, as Casey Bergman's is the answer that has helped me the most. I'm pretty sure that genomeCoverageBed from the BEDTools package is what you're looking for.