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#Welcome to the vafCorrect wiki!

If an individual has more than one tumour sample it is helpful to perform comparative analysis of variant data on multiple tumour samples in unbiased manner. This script facilitates unbiased pileup[MNV] and exonerate[Indel] based VAF calculation for union of variant sites in a set of related samples.

cgpVaf.pl -d testdir -o testdir/output -g testdir/genome.fa -a indel -e .vcf.gz -nn <normalSample> -tn <tumourSample>

Example input bed file [optional]: example bed format ###chr pos ref alt

1 16894612 T G

1 16900912 G A

1 16901539 G T