NGS Pathway analysis for Trio

Question

[nayshool]

Hi everyone!

I am looking for a tool for pathway analysis of next generation sequencing data of a trio (the child is sick with some neurological disease). Does anyone have recommended tool or tools for such a task?

Thank you

Omri

Answer 1

[Ram]

You're looking for a pipeline, not a tool. You will have to go through the routine of QC, alignment and variant calling and then use a pedigree to phase the variants, then annotate using KEGG/GO databases before moving on to pathway enrichment analyses.

[lait]

regarding the last step u mentioned, after phasing the mutations, is there a pathway analysis tool that takes into consideration if the mutations are from a paternal or a maternal origin ?

[Ram]

You might want to check out PLINK/SEQ's denovo and cnv-denovo utilities