Determining Each Samples Coverage Area
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.
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Robert Sicko
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duplicate of Calculate per exon/per gene coverage
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!
you should use the GATK-depth of coverage solution.
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.
then just see
extract alignment from very large BAM file
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.