targeted resequencing data analysis

Question

[dentepre]

Hi,

I have to perform variant calling from DNA sequencing data, but in targeted sequencing mode. My libraries were enriched by set of about 100 genes and I want to find mutations (SNV and indels among them).

What is the best way to perform this kind of analysis? Should I mapped to the whole reference human genome (like for whole exome sequencing pipelines) and then select only interested regions or just create an artificial "short" genome with only interested set of genes and then mapped to this "artificial genome"? Or completely different?

And could you recommend me some papers about analyzing data from targeted sequencing?

Best, d.

[ATpoint]

See as a starting point:

Most common practice for targeted sequencing analysis tools?

Answer 1

[WouterDeCoster]

Should I mapped to the whole reference human genome (like for whole exome sequencing pipelines) and then select only interested regions

Yes. Always align to the full genome. During variant calling you can specify which regions you are interested in, for example using the -L argument of GATK.

And could you recommend me some papers about analyzing data from targeted sequencing?

If you know about analysis from WES then this is the same, just smaller.

[ramshahaya]

Hi,

I would like to know that If I am interested in more than one chromosome, then Should I use ? -L chr 1, chr 25, chr 26