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 /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

tabix -p vcf sample_name.vcf.gz 

BCFTOOLS SORT

#BCFTOOLS SORT
bcftools sort -O z -o sample_name_sorted.vcf.gz sample_name.vcf.gz

BCFTOOLS NORM

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

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 /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

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