OncoDNA Support

Note: If you have any question or if your format is rejected, fell free to contact our team to the email address at <a href="mailto:oncokdmsales@oncodna.com" rel="nofollow noopener noreferrer" target="_blank">oncokdmsales@oncodna.com.</a>

a. Input definition VCF file must be compatible with VCF version 4.0 (or higher) specification: vcf4.0 b. Reference genome Application only support hg19/GRCh37 reference genome, if your input file was produced against hg38/GRCh38, you can use following online tool to convert genomic coordinate: • NCBI remap: <a href="https://www.ncbi.nlm.nih.gov/genome/tools/remap" rel="nofollow noopener noreferrer" target="_blank">https://www.ncbi.nlm.nih.gov/genome/tools/remap</a> Additionally to this, reported alteration on mitochondrial chromosome and patch sequenced will be filtered out as they will not lead to usable data for biological analysis. c. Sample content Input file must contain one and only one sample, if none or multiple samples are found in file, it would be rejected. d. Alteration content OncoKDM application support VCF only for small nucleotide alteration (i.e. SNV/MNV an short InsDel). All structural variations describe in input file will be filtered out.

2. SUPPORTED TOOLS (NON-EXHAUSTIVE) VCF import was tested and validated with following list of Variant caller software: • Pisces (<a href="https://github.com/Illumina/Pisces" rel="nofollow noopener noreferrer" target="_blank">https://github.com/Illumina/Pisces</a>) • TorrentServerVariantCaller (<a href="https://github.com/iontorrent/TS" rel="nofollow noopener noreferrer" target="_blank">https://github.com/iontorrent/TS</a>) • freebayes (<a href="https://github.com/ekg/freebayes" rel="nofollow noopener noreferrer" target="_blank">https://github.com/ekg/freebayes</a>) • GATK: HaplotypeCaller (<a href="https://software.broadinstitute.org/gatk/download/" rel="nofollow noopener noreferrer" target="_blank">https://software.broadinstitute.org/gatk/download/</a>) • VarScan (<a href="https://github.com/dkoboldt/varscan" rel="nofollow noopener noreferrer" target="_blank">https://github.com/dkoboldt/varscan</a>) • Samtools: BcFtools (<a href="https://github.com/samtools/bcftools" rel="nofollow noopener noreferrer" target="_blank">https://github.com/samtools/bcftools</a>) • Mutect1 (<a href="https://github.com/broadinstitute/mutect" rel="nofollow noopener noreferrer" target="_blank">https://github.com/broadinstitute/mutect</a>) • Platypus (<a href="https://github.com/andyrimmer/Platypus" rel="nofollow noopener noreferrer" target="_blank">https://github.com/andyrimmer/Platypus</a>) • CLCBio (<a href="http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current" rel="nofollow noopener noreferrer" target="_blank">http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current</a>) • Mutect2* (<a href="https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_cancer_m2_MuTect2.php" rel="nofollow noopener noreferrer" target="_blank">https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_cancer_m2_MuTect2.php</a>) • VarDict (<a href="https://github.com/AstraZeneca-NGS/VarDict" rel="nofollow noopener noreferrer" target="_blank">https://github.com/AstraZeneca-NGS/VarDict</a>) • NextGene (<a href="https://softgenetics.com/NextGENe.php" rel="nofollow noopener noreferrer" target="_blank">https://softgenetics.com/NextGENe.php</a>) • LoFreq (<a href="http://sourceforge.net/projects/lofreq/" rel="nofollow noopener noreferrer" target="_blank">http://sourceforge.net/projects/lofreq/</a>)

What are the format requirements for VCF files?

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