Coverage analysis of NGS data by Depth

Question

[nilakshafreezon]

Hello,

Can anybody please tell me a method to calculate the coverage of a NGS sequencing result (BAM File) given the sequence depth. ? For example;

For sample 1 :

Coverage at 10x = 95% Coverage at 20x = 90% Coverage at 30x = 86%

etc.

I've seen these kind of reports in Illumina Miseq Reporter, but couldn't figure out how to do that.

Thanks in advance.

[Brian Bushnell]

What kind of data do you have, and what are you trying to accomplish?

[nilakshafreezon]

I have human Exome data aligned to the GrCh37 reference as BAM files. Enriched regions are also available as a bed file. I need to get, up to what percentage the "supposed to be enriched regions" are actually covered and in what depth.

For ex:

Coverage at 10x = 95% Coverage at 20x = 90% Coverage at 30x = 86%

[GenoMax]

See: depth calculation for targeted resequencing

Answer 1

[guillaume.rbt]

Hi,

You can use bedtools to get the coverage at each base of your alignment :

bedtools genomecov -d -ibam your_bam.bam -g your_genome.fa > genome_cov.txt

Then you can use a stat tool, as R, to know the percentage of positions above or below a given depth.

Answer 2

[µbinfie]

qualimap can generate a report as you wanted. Simple command: qualimap bamqc -bam you_bam_file.bam -outfile report.pdf -outformat PDF

A portion of the report for example:

>>>>>>> Coverage

 mean coverageData = 32.3065X
 std coverageData = 48.0755X

 There is a 75.49% of reference with a coverageData >= 1X
 There is a 71.4% of reference with a coverageData >= 2X
 There is a 68.41% of reference with a coverageData >= 3X
 There is a 65.65% of reference with a coverageData >= 4X
 There is a 63.03% of reference with a coverageData >= 5X
 There is a 60.5% of reference with a coverageData >= 6X
 There is a 58.11% of reference with a coverageData >= 7X
 There is a 55.96% of reference with a coverageData >= 8X
 There is a 54.04% of reference with a coverageData >= 9X
 There is a 52.34% of reference with a coverageData >= 10X
 There is a 50.84% of reference with a coverageData >= 11X
 There is a 49.49% of reference with a coverageData >= 12X
 There is a 48.32% of reference with a coverageData >= 13X
 There is a 47.23% of reference with a coverageData >= 14X
 There is a 46.25% of reference with a coverageData >= 15X
 There is a 45.37% of reference with a coverageData >= 16X
 There is a 44.57% of reference with a coverageData >= 17X
 There is a 43.83% of reference with a coverageData >= 18X
 There is a 43.12% of reference with a coverageData >= 19X
 There is a 42.43% of reference with a coverageData >= 20X
 There is a 41.8% of reference with a coverageData >= 21X
 There is a 41.18% of reference with a coverageData >= 22X
 There is a 40.57% of reference with a coverageData >= 23X
 There is a 39.99% of reference with a coverageData >= 24X
 There is a 39.42% of reference with a coverageData >= 25X
 There is a 38.87% of reference with a coverageData >= 26X
 There is a 38.34% of reference with a coverageData >= 27X
 There is a 37.81% of reference with a coverageData >= 28X
 There is a 37.29% of reference with a coverageData >= 29X
 There is a 36.78% of reference with a coverageData >= 30X
 There is a 36.28% of reference with a coverageData >= 31X
 There is a 35.79% of reference with a coverageData >= 32X
 There is a 35.3% of reference with a coverageData >= 33X
 There is a 34.81% of reference with a coverageData >= 34X
 There is a 34.32% of reference with a coverageData >= 35X
 There is a 33.84% of reference with a coverageData >= 36X
 There is a 33.36% of reference with a coverageData >= 37X
 There is a 32.89% of reference with a coverageData >= 38X
 There is a 32.41% of reference with a coverageData >= 39X
 There is a 31.93% of reference with a coverageData >= 40X
 There is a 31.46% of reference with a coverageData >= 41X
 There is a 30.98% of reference with a coverageData >= 42X
 There is a 30.52% of reference with a coverageData >= 43X
 There is a 30.04% of reference with a coverageData >= 44X
 There is a 29.57% of reference with a coverageData >= 45X
 There is a 29.1% of reference with a coverageData >= 46X
 There is a 28.62% of reference with a coverageData >= 47X
 There is a 28.14% of reference with a coverageData >= 48X
 There is a 27.65% of reference with a coverageData >= 49X
 There is a 27.17% of reference with a coverageData >= 50X
 There is a 26.68% of reference with a coverageData >= 51X