Question: NGS Pathway analysis for Trio
gravatar for nayshool
4.9 years ago by
nayshool20 wrote:

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



snp tool next-gen • 1.4k views
ADD COMMENTlink modified 4.9 years ago by _r_am31k • written 4.9 years ago by nayshool20
gravatar for _r_am
4.9 years ago by
Baylor College of Medicine, Houston, TX
_r_am31k wrote:

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.

ADD COMMENTlink modified 11 months ago • written 4.9 years ago by _r_am31k

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 ?

ADD REPLYlink written 3.0 years ago by lait150

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

ADD REPLYlink written 3.0 years ago by _r_am31k
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