DeCa

DeCa is a high-performance, attention-based tool designed for the rapid and accurate detection of somatic variants.

Prerequisite

• htslib : The library to read hts files.
• boost : Boost provides free peer-reviewed portable C++ source libraries.
• libtorch : An open source machine learning framework that accelerates the path from research prototyping to production deployment.

Building DeCa

build the code from a Git repository requires following steps:

git clone https://github.com/536260668/DeCa
cd Deca
mkdir release
cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_MAKE_PROGRAM=ninja -G Ninja -S /your/path/to/DeCa -B /your/path/to/DeCa/release
cmake --build /your/path/to/DeCa/release -j <threads>

By default, this will build against an HTSlib source tree in ../htslib. this program need libtorch in /usr/libtorch to run.

Docker Image

You can download the docker image using the following command:

docker pull registry.cn-hangzhou.aliyuncs.com/de-ca/de-ca:latest

Running DeCa

Parameters

Required Arguments:

• --input, -I:String
  BAM/SAM/CRAM file containing reads. This argument must be specified at least once.
  Required

• --output, -O:File
  The output recalibration table file to create.
  Required

• --reference, -R:String
  Reference sequence file.
  Required

• --normal:String
  BAM sample name of normal(s).
  Required

Optional Arguments:

• --callable-depth:Int
  Minimum depth to be considered callable for Mutect stats. Does not affect genotyping.
  Default: 10

• --max-prob-propagation-distance:Int
  Upper limit on how many bases away probability mass can be moved when calculating the boundaries between active and inactive assembly regions.

• --active-probability-threshold:Float
  Minimum probability for a locus to be considered active.
  Default: 0.002

• --assembly-region-padding:Int
  Number of additional bases of context to include around each assembly region.
  Default: 100

• --max-assembly-region-size:Int
  Maximum size of an assembly region.
  Default: 300

• --min-assembly-region-size:Int
  Minimum size of an assembly region.
  Default: 50

• --bqsr-with-mutect
  Add ApplyBQSR into this tool. If set, --tumor-table and --normal-table are required.

• --tumor-table:File
  Recalibration table for tumor reads, generated in the BaseRecalibrator part.

• --normal-table:File
  Recalibration table for normal reads, generated in the BaseRecalibrator part.

• -T:Int
  Size of thread pool.

• -L:String
  Specifies the name of the chromosome to be processed.

• -M:String
  Path to the machine learning model.

• --max-reads-per-alignment-start-M:Int
  Maximum number of reads to retain per alignment start position. Reads above this threshold will be downsampled. Set to 0 to disable.

Example

./Deca -R reference.fa \
-I tumor.bam \
-I normal.bam \
-O output.vcf \
-T 64 \
--normal normal \
-M trans.pt \
-L 10