Question: Copy Number Variation Steps (CNVs) - detection step by step
1
gravatar for elsayedhegazy
2.8 years ago by
elsayedhegazy20 wrote:

Dear friends, I need to know the detailed steps of CNVs detection from NGS data (FASTQ , BAM, SAM or VCF). If i have one of these files what can i do to extract the copy number variation. i am not talking about tool names i need the algorithm steps.

Regards, elsayed

cnvs snp sequence ngs genome • 2.1k views
ADD COMMENTlink modified 2.8 years ago by Medhat8.2k • written 2.8 years ago by elsayedhegazy20

you are asking about the work flow how to get CNV from fastq file for example>?

ADD REPLYlink written 2.8 years ago by Medhat8.2k

Yes but with explanation of steps some like from FASTQ or VCF file we search for something after that we filter it using something

if you have one script code show all steps you are most welcome to post it here

Thanks a millions

ADD REPLYlink written 2.8 years ago by elsayedhegazy20
2
gravatar for Chirag Nepal
2.8 years ago by
Chirag Nepal2.2k
Copenhagen
Chirag Nepal2.2k wrote:

Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.

ADD COMMENTlink written 2.8 years ago by Chirag Nepal2.2k

Thanks Chirag, Still little bit confused these steps to run tools in proper way. My need is algorithm steps as concepts or theoretical steps - How to know this region contain CNV and how to extract it

ADD REPLYlink written 2.8 years ago by elsayedhegazy20
2
gravatar for Medhat
2.8 years ago by
Medhat8.2k
Texas
Medhat8.2k wrote:

Ok, If the question is about workflow her it is:

enter image description here


for algorithm you can read https://en.wikipedia.org/wiki/SNV_calling_from_NGS_data

and for in depth details: Review of alignment and SNP calling algorithms for next-generation sequencing data

A framework for variation discovery and genotyping using next-generation DNA sequencing data

for script you can follow this tutorial

Variant calling workflow - shell script

Workflow Or Tutorial For Snp Calling?

https://gencore.bio.nyu.edu/variant-calling-pipeline/

http://userweb.eng.gla.ac.uk/cosmika.goswami/snp_calling/SNPCalling.html

Good luck.

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by Medhat8.2k

Thanks a million medhat i will explore these links

ADD REPLYlink written 2.8 years ago by elsayedhegazy20
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