find areas of very low and extra high coverage in NGS data

[willMD]

Are there any tools that can report all areas of very low coverage or areas of high coverage in NGS data?

[dkatzel]

I've written some custom code to programatically do this, but it only works on a few assembly formats (don't have time or funding to add more formats yet). But several assembler programs have ways to output the coverage levels of the contigs. It would then be up to you to parse that output and find any locations that are below or above your thresholds.

[suryasaha]

A commonly used method is to map all your reads to contigs using bowtie2/bwa mem/bwa and calculate the coverage with samtools or bedtools.

[jimmybee]

Are there any tools that can report all areas of very low coverage or areas of high coverage in NGS data?

Can you give us some more information? What type of data do you have? Have you mapped reads to a reference yet?

If you do have a bam file of aligned reads to a reference sequence then you will be able to generate a plot of the per-base coverage of the reference sequence using bedtools genomeCoveragebed.

[willMD]

Human whole genome data aligned to hg19 in bam file. Thanks. I'll look at bedtools.