Output files and formats

CTAT-mutations Output Files and Formats

Following are the column headers and its description:

Column	Description
CHROM	Chromosome
POS	The 1-based position of the variation on the given sequence.
REF	Base(s) at position in the reference genome (hg38)
ALT	Alternate base(s)
GENE	Gene name DP - combined depth across samples
QUAL	A quality score associated with the inference of the given alleles.
MQ	RMS mapping quality
SAO	An integer that indicates variant allele origin. The accepted values for this tag are: 0 - unspecified, 1 - Germline, 2 - Somatic, 3 - Both. Note: "SAO" is "SNP Allele Origin". We have changed "SNP" to the more inclusive term "variant"; the tag "SAO" remains in the vcf files.
NSF	The consequence of the variation is a non-synonymous frameshift -- a coding region variation where one allele in the set changes all downstream amino acids.
NSM	The consequence of the variation is a non-synonymous (missense) change -- it is a coding region variation where one allele in the set changes the amino acid, but translation continues.
NSN	The consequence of the variation is a non-synonymous stop codon (nonsense) -- it is a coding region variation where one allele in the set changes to a STOP codon (TER or *).
TUMOR	Tumor type
TISSUE	tissue name
COSMIC_ID	COSMIC database ID
KGPROD	Indicates the variation was submitted as part of the 1000 Genomes Project
RS	The consequence of the variation is a non-synonymous frameshift -- a coding region variation where one allele in the set changes all downstream amino acids.
PMC	Indicates that links exist from the variant's rs record to a PubMed Central article.
CHASM_PVALUE	Empirical p-value (probability that passenger variant is misclassified as a driver).
CHASM_FDR	False discovery rate expected (Benjamini-Hochberg multiple testing correction).
VEST_PVALUE	Empirical p-value (probability that benign variant is misclassified as pathogenic).
VEST_FDR	Composite false discovery rate (Benjamini-Hochberg multiple testing correction) for non-silentvariants in the gene combined with Stouffer’s Z-score method.

Description of all outputs

File	Description
cancer.tab	CRAVAT generated VCF file converted to user friendly tab delimited format
cancer.vcf	CRAVAT generated VCF file
variants.vcf	Output from GATK’s Haplotype caller in VCF format with raw, unfiltered SNP and indel calls
variants.vcf.idx	Indexed variants.vcf file
refGene.sort.bed	Reference sorted BED file
variants_initial_filtering.vcf	Initially filtered variants file by VariantFiltration in GATK4.
variants_initial_filtering.vcf.idx	Indexed filtered vcf file
variants_initial_filtering_clean_snp_RNAedit.vcf.gz	RNAedit variant filters REDIportal and RADAR applied.
variants_initial_filtering_clean_snp_RNAedit.vcf.gz.csi	Indexed filtered RNAedit filter applied file
variants_initial_filtering_clean_snp_RNAedit.vcf_dbsnp.vcf.gz	BCFtools annotated DBSNP variants filtered file
variants_initial_filtering_clean_snp_RNAedit.vcf_snpeff.vcf	Filtered VCF file snpeff annotated
variants_initial_filtering_clean_snp_RNAedit.vcf_snpeff_updated.vcf.gz	snpeff annotated variants filtered file
variants_initial_filtering_clean_snp_RNAedit.vcf_snpeff_updated.vcf.gz.csi	Indexed snpeff annotated variants filtered file
annotated_min_filtered.vcf.gz	BCFtools annotated file obtained from CRAVAT generated VCF output
mutation_inspector.json	JSON file including all mutations, required for visualization