File formats

This script is designed to work on Linux high performance computing clusters, however it will also work on Macs and Linux computers; at present it will not work on PCs since.

The script should be able to assess any BAM file that includes human exome sequences with good coverage (>10x); it will cope with changes in chromosome naming (i.e. 'chr21' vs. '21').

The FinalReports from Illumina SNP genotyping need to be formatted from GenomeStudio in a specific format with one file per person with the following columns in this order:

#SampleID
#SNP Name
#Chr
#Position
#Allele1 – Top
#Allele2 – Top
#Theta
#R
#B Allele Freq
#Log R Ratio

The top of you FinalReport file should look something like this:

FR_format.jpg

For instructions on making correctly formatted FinalReports see Making FinalReports.

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