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NGS Pathway analysis for Trio

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

next-gen snp
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updated by Ram Ram • written by nayshool • nayshool

1 answer

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.

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written by Ram Ram

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 ?

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written by lait lait

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

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written by Ram Ram

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