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Table 6 List of software components utilized in the benchmarking workflow with their software dependencies, settings and Docker image names (as available in the Docker Hub repository) if applicable

From: Benchmarking workflows to assess performance and suitability of germline variant calling pipelines in clinical diagnostic assays

Software component

Docker image

Other software dependencies and settings included

hap.py v0.2.10

sowmiu/happy

Ubuntu 14.04

Python 2.7.6, python2.7-dev, python-software-properties, cython, numpy, pandas, setuptools, pybedtools, pysam, bx-python, nose, pip, numpy, Distribute

Cmake > 2.8, gcc/g++4.8 + zlib1g-dev, libncurses5-dev, bzip2, wget, libbz2-dev, build-essential, libatlas-base-dev, pkg-config, boost 1.55 + , software-properties-common

git, samtools 0.1.19, bcftools 0.1.19, gfortran

bcftools

vandhanak/bcftools:1.3.1

Ubuntu 14.04

Make, g++, gcc, zlib1g-dev, libgsl0ldbl, gsl-bin, libgsl0-dev, libatlas-base-dev git, htslib 1.3.2

IndelSizeDistribution_Detailed.R

vandhanak/rbase:3.3.2

Ubuntu 14.04

libcurl4-openssl-dev, libxml2-dev, locale setting: en_US.UTF-8

Set access to these repositories: trusty-backports, CRAN

Benchmarking_truth_set.py

–

Python 2.7

Verify_variants.py

–

Python 2.7