A next-generation sequencing assay designed to cover 179 cancer-associated genes predicting sensitivity or resistance to various types of anti-cancer therapy. The genes were selected from Cancer Gene Census based on their involvement in drug response and include biomarkers from NCCN and ESMO guidelines. The panel is eligible for detecting all classes of mutations (indels, substitutions, amplifications, and rearrangements) as well as TMB, LOH, and MSI in a single DNA workflow. MiniTest 179 can be used for blood and FFPE DNA to assess germline and somatic variants.
Install Snakemake:
pip install snakemake
Install GATK:
wget https://github.com/broadinstitute/gatk/releases/download/4.2.2.0/gatk-4.2.2.0.zip
unzip gatk-4.2.2.0.zip
# export PATH="/path/to/gatk-4.2.2.0:$PATH"
Install SnpEff:
wget https://sourceforge.net/projects/snpeff/files/snpEff_v4_3t_core.zip/download
unzip snpEff_v4_3t_core.zip
echo -e '#!/bin/sh\njava -jar -Xmx8G /path/to/snpEff/snpEff.jar $@' > ~/bin/snpEff
chmod a+x ~/bin/snpEff
echo -e '#!/bin/sh\njava -jar -Xmx8G /path/to/snpEff/SnpSift.jar $@' > ~/bin/SnpSift
chmod a+x ~/bin/SnpSift
Install bedtools:
wget https://github.com/arq5x/bedtools2/releases/download/v2.30.0/bedtools.static.binary
mv bedtools.static.binary ~/bin/bedtools
Install samtools and bcftools:
wget https://github.com/samtools/samtools/releases/download/1.14/samtools-1.14.tar.bz2
wget https://github.com/samtools/bcftools/releases/download/1.14/bcftools-1.14.tar.bz2
tar jvfx samtools-1.14.tar.bz2
tar jvfx bcftools-1.14.tar.bz2
cd samtools-1.14
./configure
make
cp samtools ~/bin/
cd ../bcftools-1.14
./configure
make
cp bcftools ~/bin/
cd ..
Get CADD, GnomAD, and ClinVar databases and set path to them in the Snakefile.
Run snakemake in the directory with Snakefile
, Tumor.bam
, Blood.bam
, and Tumor.bed:
snakemake -j40 Tumor_vsn_Blood_TMB.txt
The Tumor.bed
is a symbolic link to UTTV3_capture_targets_GRCh38.bed
ln -s UTTV3_capture_targets_GRCh38.bed Tumor.bed
The study has been supported by the Russian Science Foundation (21-75-30015).