snps_and_indels.cwl Output Files

tumor_id.normal_id.vardict.vcf - Vardict VCF
tumor_id.normal_id.mutect.txt - Mutect txt
tumor_id.normal_id.mutect.vcf - Mutect VCF

tumor_id.normal_id.mutect_STDfilter.norm.vcf.gz - Gzipped VCF file from mutect after basic_filtering based on VCF field filters
tumor_id.normal_id.mutect_STDfilter.norm.vcf.gz.tbi - index for mutect Gzipped VCF after basic_filtering
tumor_id.normal_id.vardict_STDfilter.norm.vcf.gz - Gzipped VCF file from vardict after basic_filtering based on VCF field filters
tumor_id.normal_id.vardict_STDfilter.norm.vcf.gz.tbi - index for vardict Gzipped VCF after basic_filtering

tumor_id.normal_id.combined-variants.vcf - Merged Mutect and Vardict calls

tumor_id.normal_id.combined-variants.vep.maf - VCF has been converted to MAF file using VCF2MAF, includes VEP annotations

tumor_id.normal_id.combined-variants_anno.vcf - Annotated after combining VCFs
tumor_id.normal_id.combined-variants.vep_droppedNGRrmv.maf - Dropped Non-genomic region calls
tumor_id.normal_id.combined-variants.vep_droppedrmv.maf - Dropped for other reasons calls
tumor_id.normal_id.combined-variants.vep_keptrmv.maf - Kept after remove_variants module

tumor_id.normal_id.combined-variants.vep_keptrmv_taggedHotspots.maf - Tagged hotspots
tumor_id.normal_id.combined-variants.vep_keptrmv_taggedHotspots_fillout.maf - Genotyped MAF

tumor_id.normal_id.combined-variants.vep_keptrmv_taggedHotspots_fillout_filtered.maf - Filtered through custom ACCESS_filters module
tumor_id.normal_id.combined-variants.vep_keptrmv_taggedHotspots_fillout_filtered_condensed.maf - Condensed file to just mutations that pass filters