/usr/bin/vardict/bin/VarDict -f "0" \
-c "1" \
-g "5" \
-E "3" \
-S "2" \
-G /path/to/reference_fasta.ext \
-N sample_name \
-b /path/to/bam/file.bam \
-bedfile /path/to/bedfile.ext \
> vardict_app_output.vcfRscript /usr/bin/vardict/bin/teststrandbias.R > output_teststrandbias.var \
< /path/to/input_vardict.varperl /usr/bin/vardict/bin/var2vcf_valid.pl \\
-N sample_name
-f 0
> output_vcf_name
< /path/to/input_vardict.varpv vardict single filter -i /path/to/input_vardict.vcf \
--tsampleName sample-name \
-ad 1 \
-fg false \
-mq 0 \
-tnr 1 \
-dp 20 \
-vf 5e-05 bgzip -c /path/to/input_single_filter.vcf > sample_name.vcf.gztabix -p vcf sample_name.vcf.gz #BCFTOOLS SORT
bcftools sort -O z -o sample_name_sorted.vcf.gz sample_name.vcf.gzbcftools norm --check-ref s \
-m + \
-O z \
-o sample_name_norm.vcf.gz \
-f /path/to/ref_fasta.fa \
sample_name_sorted.vcf.gzbcftools concat -a -O z \
-o sample_name_merged.vcf \
sample_name_sorted.vcf.gz sample_name_complex_sorted.vcf.gzjava -jar /snpEff/SnpSift.jar annotate -c snpeff.config \
/cosmicData/CosmicCodingMuts.vcf.gz sample_name_merged.vcf > sample_name_prevalence.vcfperl /opt/vcf2maf-1.6.21/vcf2maf.pl \
--output-maf sample_name_vcf2maf.maf \
--custom-enst /regions_of_interest/current/dmp_ACCESS-panelA-v1-isoform-overrides \
-maf-center mskcc.org \
--min-hom-vaf 0.7 \
--ncbi-build GRCh37 \
--ref-fasta /path/to/ref_fasta.fa \
--retain-info "set,TYPE,FAILURE_REASON" \
--species homo_sapiens_merged \
--tumor-id sample_name \
--vcf-tumor-id sample_name \
--vep-path /usr/local/bin/ \
--vep_data /.vep/ \
--input-vcf sample_name_snpsift.vcfpython3 /oncokb/MafAnnotator.py -o sample_name_oncokb.maf \
-b /path/to/API_toke.txt \
-a TRUE \
-i sample_name_vcf2maf.mafpv maf annotate mafbybed -m sample_name_oncokb.maf \
-b /path/to/bed_file.bed \
-c "column_name" \
-o sample_name_mafbybed.mafpv maf annotate mafbytsv -m sample_name_mafbybed.maf \
-b /path/to/tsv_file.tsv \
-c "column_name" \
-o sample_name_mafbytsv.mafpv maf tag cmo_ch -m sample_name_mafbytsv.maf \
-o sample_name_maf_tagged.mafpv maf filter cmo_ch -m sample_name_maf_tagged.maf \
-o sample_name_maf_filter.maf