Fu Po-Ying

hail + VEP + gnomad

ubuntu 20.04, Python 3.9.5, Miniconda 4.10.3, snakemake 6.6.1, bgzip 1.13

Snakemake 7.19.1, Conda 22.11.1, Clara Parabricks 4.0.0-1

Parabricks v3.6, miniconda v4.12.0, snakemake v7.6.2

fastq_pair v1.0 (https://github.com/linsalrob/fastq-pair), snakemake-minimal v7.14.2

Ubuntu 18.04, Python 3.6.9, Hail 0.2.78 with notebook 6.4.6 or snakemake 6.10.0

bcftools 1.12 install using Conda 4.10.1

Using snakemake stable image (v7.6.2) with conda 4.12.0, bamMetrics and samtools v1.11

Hail 0.2.79-f141af259254, Apache Spark version 3.1.2, pip 20.0.2, python 3.8.10,

LASER v2.04, TRACE v1.03, samtools 1.11, Python 2.7.18, R version 4.1.2 (2021-11-01)

Ubuntu 20.04, Python 3.8.10, JVM 11, PySpark 3.1.2, Glow, Hail, pip3

VEP 104, Perl v5.30, Java 11, Miniconda 3, Python 3.7, bgzip v1.9

Ubuntu 20.04, Open JDK 11, Miniconda3, Python 3.7.10, Apache Spark version 2.4.1, pyspark-2.4.1

Triodenovo v0.0.6 and v0.0.4

Miniconda 3, R v3.6.0, Jupiter Notebook

Ubuntu 20.04, JAVA JDK11, Miniconda3 v4.9.2, Python v3.8, Nextflow 19.01.0.5050, R v4.1.0

ENV for VirMutSig: Ubuntu 20.04, Nextflow 21.04.0, Miniconda 4.10.3, R v4, Java 8

samtools 1.11

Parabricks v3.5.0.1 with snakemake v6.6.0 (for Snakemake use only)

plink2 installed using Conda

Python 2.7 && conda 4.8.4 && samtools 1.11