> For the complete documentation index, see [llms.txt](https://cmo-ci.gitbook.io/chip-variant-calling-and-processing/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cmo-ci.gitbook.io/chip-variant-calling-and-processing/usage-of-individual-commands.md). # Usage of individual commands **Vardict v1.8.2** 
/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.vcf
``` Rscript /usr/bin/vardict/bin/teststrandbias.R > output_teststrandbias.var \ < /path/to/input_vardict.var ``` ```perl perl /usr/bin/vardict/bin/var2vcf_valid.pl \\ -N sample_name -f 0 > output_vcf_name < /path/to/input_vardict.var ``` **pv vardict v0.1.5** ``` pv 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 ``` **BCFTOOLS v 1.15.1** **BGZIP** 
bgzip -c /path/to/input_single_filter.vcf > sample_name.vcf.gz
**TABIX** ```bash tabix -p vcf sample_name.vcf.gz ``` **BCFTOOLS SORT** ```bash #BCFTOOLS SORT bcftools sort -O z -o sample_name_sorted.vcf.gz sample_name.vcf.gz ``` **BCFTOOLS NORM** ```bash bcftools norm --check-ref s \ -m + \ -O z \ -o sample_name_norm.vcf.gz \ -f /path/to/ref_fasta.fa \ sample_name_sorted.vcf.gz ``` **BCFTOOLS CONCAT** ```bash bcftools concat -a -O z \ -o sample_name_merged.vcf \ sample_name_sorted.vcf.gz sample_name_complex_sorted.vcf.gz ``` **SNPSIFT annotation v5.0:** 
java -jar /snpEff/SnpSift.jar annotate -c snpeff.config \
/cosmicData/CosmicCodingMuts.vcf.gz sample_name_merged.vcf > sample_name_prevalence.vcf
**vcf2maf v1.6.21** ```perl perl /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.vcf ``` **oncoKB annotator v3.2.2** ```python python3 /oncokb/MafAnnotator.py -o sample_name_oncokb.maf \ -b /path/to/API_toke.txt \ -a TRUE \ -i sample_name_vcf2maf.maf ``` **PV modules v0.2.3** **MAF annotate by BED** ``` pv maf annotate mafbybed -m sample_name_oncokb.maf \ -b /path/to/bed_file.bed \ -c "column_name" \ -o sample_name_mafbybed.maf ``` **MAF annotate by TSV** ``` pv maf annotate mafbytsv -m sample_name_mafbybed.maf \ -b /path/to/tsv_file.tsv \ -c "column_name" \ -o sample_name_mafbytsv.maf ``` **MAF tag** ``` pv maf tag cmo_ch -m sample_name_mafbytsv.maf \ -o sample_name_maf_tagged.maf ``` **MAF filter** 
pv maf filter cmo_ch -m sample_name_maf_tagged.maf \
    -o sample_name_maf_filter.maf
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