Q:
We are interested in using the HotCommics pipeline to identify hotspot
communities from our own cancer mutation data. However, we have
difficulty in running the pipeline because we could not find
description of the input files in the snpMapping and the
hotSpotCalculation step. Could you kindly help to provide us some
example input files so that we can appropriately format our input?

A:
Thank you for your interest in our work. The input file for SNP
mapping step is the input file for VAT tool, which can be the vcf file
that you. are working with. Alternatively, you can also use a
tab-separated file with header information described below.

#CHROM hg19_pos ID Ref Alt Tumor_Sample_Barcode
Matched_Norm_Sample_Barcode Info

http://vat.gersteinlab.org

For the hotspot community identification, you will have to run the
community identification module for each PDBs on which your mutations
have mapped to

https://github.com/gersteinlab/HotCommics/tree/master/communityIdentification

Once you have generated these communities and have a list of PDBs on
which mutations have mapped to then you will need to provide the list
of PDBs for hotspot calculation.