Calculates coverage metrics for a given BAM file.
This app may be executed as a standalone app.
Required input files:
- A BAM file (
.bam), - A corresponding index file (
.bai), - Quality Flag (
boolean; default:true) - When calculating coverage to get a more accurate calculation it is required to discount multi mapped reads (those with a MAPQ of 0), and duplicate reads. This is done by default with the Quality Flags input parameter, but may be included by setting to False. - Mosdepth Docker image (
tar.gz)
Optional input: - Optional arguments (
string) - as described in the docs: https://github.com/brentp/mosdepth. - A bed file, optional (
.bed) - Usage of bed file does not require passing any additional flags as per the docs, it just requires that the bed file is passed as the bed input. - Quantize label (
string) -
Usage of the "--quantize" option also has optional labels as an input. By default if none are given and 4 bins are passed, the default labels from the docs are used. For ≠ 4 bins or custom labels, this should be passed as a comma seperated list in "quantize_labels".
e.g. For the following 6 bins:
--quantize 0:1:4:50:100:200:
The following label option would be passed:
"label1, label2, label3, label4, label5, label6"
This app outputs:
{prefix}.mosdepth.global.dist.txt{prefix}.mosdepth.summary.txt{prefix}.mosdepth.region.dist.txt(if --by is specified){prefix}.per-base.bed.gz(unless -n/--no-per-base is specified){prefix}.regions.bed.gz(if --by is specified){prefix}.quantized.bed.gz(if --quantize is specified){prefix}.thresholds.bed.gz(if --thresholds is specified)reference_build.txt
dx run eggd_mosdepth \
-ibam=file-xxxx \
-iindex=file-xxxx \
-imosdepth_docker=file-xxxx
This is the source code for an app that runs on the DNAnexus Platform. For more information about how to run or modify it, see https://documentation.dnanexus.com/.