Mutation effect on sites (analysis)

Find transcription factor binding sites affected by mutations.

Input VCF track – Input track in VCF format
Genome – Reference genome
- Sequences source – Select database to get sequences from or 'Custom' to specify sequences location manually
- Sequence collection – Specify path to folder containing sequences if 'Custom' sequences source is selected
Profile – Predefined set of site models
Score type – The type of position weight matrix score
Score difference – Minimal site score difference between reference and alternative sequences
Independent variations – Treat each variation independently
Target gene TSS upstream – When searching for target genes, match TF binding sites to this distance upstream of TSS.
Target gene TSS downstream – When searching for target genes, match TF binding sites to this distance downstream of TSS.
One nearest target gene – Report only one target gene nearest to TSS.
Output table – Output table
Site gain track – Resulting track with site gain events
Site loss track – Resulting track with site gain events
Important mutations – Track of mutations that affects binding sites
Summary table – Summary table giving site model frequencies per mutation