FATHMM-indel predicts the functional class, pathogenic or neutral, of small indels throughout the whole non-coding genome. For each test variant, FATHMM-indel computes a standardised score that can be used to predict the functional effect and prioritise non-coding indels. For further details, please refer to the following publications.

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References

1. Michael Ferlaino, Mark F Rogers, Hashem A Shihab, Matthew Mort, David N Cooper, Tom R Gaunt, Colin Campbell.
 An integrative approach to predicting the functional effects of small indels in non-coding regions of the human genome. BMC Bioinformatics (2017), 18:442.

2. Hashem A Shihab, Mark F Rogers, Julian Gough, Matthew Mort, David N Cooper, Ian N M Day, Tom R Gaunt, Colin Campbell.
 An integrative approach to predicting the functional effects of non-coding and coding sequence variation. Bioinformatics (2015), 31:1536-1543.

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Submitting a batch of mutations

FATHMM-indel accepts batch files in variant call format (VCF). Please only provide the columns named "CHROM", "POS", "REF", and "ALT", separated by a "tab" character. These are the only fields required by the web server to score an indel. For example, a three nucleotide deletion on chromosome 13 must be submitted as:

13    39448742    TAAC    T

Please note how the field "POS" refers to the position of the fist nucleotide for the wildtype string "REF". Similarly, a three nucleotide insertion on chromosome 20 must be input as:

20    55048496    T    TGAG

An example of VCF file that can be used to upload variants can be found here.

FATHMM-indel has been trained on and classifies mutations based on the human genome assembly GRCh37.

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Browse the variant file on your local machine using the "Choose File" button and submit by pressing "Upload". The file download will start automatically once all computations are completed.

Please limit your batch file to a maximum of 10 000 indels.