Still using GRCh37/hg19? help
CRAVAT 5 is in GRCh38/hg38. If you need to annotate GRCh37/hg19 variants, check the hg19 box under Input section or use CRAVAT 4 which is in GRCh37/hg19.
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Check for VCF-format input example.
Check for CRAVAT-format input example.

Enter variants below:help
Two input formats are supported: CRAVAT format and VCF format.

VCF format
See VCF specification for details.

CRAVAT format
See input format help for details.

Genomic-coordinate input format
UID, chromosome, position (1-based), strand, reference base(s), alternate base(s), and (optional) sample ID, separated by a space or tab. UID should not contain commas. For indels, use the following format. "-" means no base. Examples are below.
VAR1 chr22 25115449 + A G Sample1 (substitution)
VAR2 chr22 25115449 + - GA Sample2 (insertion)
VAR3 chr22 25115449 + GCA - Sample3 (deletion)

Transcript-coordinate input format
Variant ID, transcript identifier, amino-acid substitution, and (optional) sample ID, separated by a space or tab. An example is below.
VAR4 NP_001135977 R641W 1 (substitution)

or upload a variant file:help
Two input formats are supported: CRAVAT format and VCF format.

VCF format
See VCF specification for details.

CRAVAT format
See input format help for details.

Genomic-coordinate input format
UID, chromosome, position (1-based), strand, reference base(s), alternate base(s), and (optional) sample ID, separated by a space or tab. UID should not contain commas. For indels, use the following format. "-" means no base. Examples are below.
VAR1 chr22 25115449 + A G Sample1 (substitution)
VAR2 chr22 25115449 + - GA Sample2 (insertion)
VAR3 chr22 25115449 + GCA - Sample3 (deletion)

Transcript-coordinate input format
Variant ID, transcript identifier, amino-acid substitution, and (optional) sample ID, separated by a space or tab. An example is below.
VAR4 NP_001135977 R641W 1 (substitution)


hg19 help
If genomic-coordinates are used for variants,
they are assumed to be in hg38.
To use hg19 instead, check this box.
red squareChoose analysis program
  VEST-4help
VEST (Variant Effect Score Toolkit)
is a method that predicts the pathogenic effect of a variant.
For more information, click here

  CHASM-3.1help
CHASM (Cancer-specific High-throughput Annotation of
Somatic Mutations) is a method that predicts the
functional significance of somatic missense variants
observed in the genomes of cancer cells, allowing variants
to be prioritized in subsequent functional studies,
based on the probability that they confer increased
fitness to a cancer cell.
For more information, click here

  GeneCard and PubMed annotationhelp
Check if want GeneCard and PubMed annotation of
the genes containing the submitted variants.
Send the analysis reporthelp to:
An excel file where analysis results
are organized into tabs.

Include text reportshelp
Additional tab-delimited text files for
easy programmatic processing
will also be included.