lethalfang/jointsnvmix2 repository overview

⁠Example script: converting JointSNVMix2's original output into VCF format recognized by SomaticSeq

docker run -v /:/mnt -i lethalfang/jointsnvmix2:0.7.5
/opt/JointSNVMix-0.7.5/build/scripts-2.7/jsm.py train joint_snv_mix_two
--convergence_threshold 0.01
--skip_size 200
/mnt/ABSOLUTE/PATH/TO/GRCh38.fa
/mnt/ABSOLUTE/PATH/TO/Matched_Normal.bam
/mnt/ABSOLUTE/PATH/TO/Tumor.bam
/opt/JointSNVMix-0.7.5/config/joint_priors.cfg
/opt/JointSNVMix-0.7.5/config/joint_params.cfg
/mnt/ABSOLUTE/PATH/TO/RESULTS/jsm.parameter.cfg

echo -e '##fileformat=VCFv4.1' > /ABSOLUTE/PATH/TO/RESULTS/JointSNVMix2.vcf echo -e '##INFO=<ID=AAAB,Number=1,Type=Float,Description="Probability of Joint Genotype AA in Normal and AB in Tumor">' >> /ABSOLUTE/PATH/TO/RESULTS/JointSNVMix2.vcf echo -e '##INFO=<ID=AABB,Number=1,Type=Float,Description="Probability of Joint Genotype AA in Normal and BB in Tumor">' >> /ABSOLUTE/PATH/TO/RESULTS/JointSNVMix2.vcf echo -e '##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">' >> /ABSOLUTE/PATH/TO/RESULTS/JointSNVMix2.vcf echo -e '##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">' >> /ABSOLUTE/PATH/TO/RESULTS/JointSNVMix2.vcf echo -e '#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNORMAL\tTUMOR' >> /ABSOLUTE/PATH/TO/RESULTS/JointSNVMix2.vcf

docker run -v /:/mnt -i lethalfang/jointsnvmix2:0.7.5
/opt/JointSNVMix-0.7.5/build/scripts-2.7/jsm.py classify joint_snv_mix_two
/mnt/ABSOLUTE/PATH/TO/GRCh38.fa
/mnt/ABSOLUTE/PATH/TO/Matched_Normal.bam
/mnt/ABSOLUTE/PATH/TO/Tumor.bam
/mnt//ABSOLUTE/PATH/TO/RESULTS/jsm.parameter.cfg
/dev/stdout | awk -F "\t" 'NR!=1 && $4!="N" && $10+$11>=0.95' |
awk -F "\t" '{print $1 "\t" $2 "\t.\t" $3 "\t" $4 "\t.\t.\tAAAB=" $10 ";AABB=" $11 "\tRD:AD\t" $5 ":" $6 "\t" $7 ":" $8}'
| docker run -v /:/mnt -i lethalfang/jointsnvmix2:0.7.5
/opt/vcfsorter.pl /mnt//ABSOLUTE/PATH/TO/GRCh38.dict - >> /ABSOLUTE/PATH/TO/RESULTS/JointSNVMix2.vcf