How to calculate average depth for each Amplicon in targeted amplicon sequencing?

Question

[bioinfo89]

Hello,

I am working with targeted amplicon sequencing data for 200 samples! I want to calculate the average depth per amplicon? I tried bedtools coverage, but it gives total number of reads which map to the target region and I am not sure if that is the average depth. It is little confusing to me.

command used:

/home/tools/bedtools2/bin/bedtools coverage -a ../../amplicon_coords.bed -b sample1_RG_sorted_indexed.bam

Is there any other way or any modified way to use bedtools coverage option to calculate the average depth per amplicon?

Any help will be appreciated.

Thanks!!

[WouterDeCoster]

I recently saw some things about ampvis2, which might be of interest for you, see for example this blog post.

Answer 1

[Pierre Lindenbaum]

I wrote bamstats04: http://lindenb.github.io/jvarkit/BamStats04.html

$ java -jar dist/bamstats04.jar -B src/test/resources/toy.bed.gz src/test/resources/toy.bam 2> /dev/null | column -t 

#chrom  start  end  length  sample  mincov  maxcov  meancov  mediancov  nocoveragebp  percentcovered
ref     10     13   3       S1      3       3       3.0      3.0        0             100
ref2    1      2    1       S1      2       2       2.0      2.0        0             100
ref2    13     14   1       S1      6       6       6.0      6.0        0             100
ref2    16     17   1       S1      6       6       6.0      6.0        0             100

[bioinfo89]

Thanks @Pierre Kindenbaum!! It is very helpful!! Also easy to understand!

[WouterDeCoster]

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

Answer 2

[601435543]

you can try GATK's DOC https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_coverage_DepthOfCoverage.php#--countType

Answer 3

[shivupatel19]

I am getting this type of results by following your command of bamstats... am confused with the coverage..how can i describe it. please help

#chrom start end length  sample mincov maxcov avgcov_0 mediancov_0 nocoveragebp_0 percentcovered_0
chr6  88278254 88278533 279     44      104     207   183.3763440860215      206.0      0     100
chr6  88278254 88278533 279     88      120     244   210.26164874551972     241.0      0     100
chr6  88278254 88278533 279     45      70      142   122.12544802867383     142.0      0     100