Should I specify exome region to do the QC with qualimap2 for WES analysis?

Question

[maria2019]

I am doing WES analysis and want to do the QC after the realignment around the indels with qualimap2. My question is should I only use hg38 to see the coverage or I should also add a .bed file consisting the information of ONLY exons?

[ATpoint]

Changed to Question rather than Page or Tool, please leave it like that.

Answer 1

[h.mon]

You should include a bed file with the targets captured by the exome out you used, not the "true" whole exome. Mapping rate inside and outside regions is an important quality metric for exome sequencing.

[maria2019]

Thank you for your response. I am very new in NGS analysis. How can I create the bed file then? Previously what I did was going to genome browser table (http://genome.ucsc.edu/cgi-bin/hgTables?hgta_doMainPage=Back) and chose exons option for the output as a bed file. Is that what you mean? Or I will have to create my own bed file?

[ATpoint]

The company that produced the capturing beads must provide this information. Either ask the wetlab staff who made the data for it or go to the methods section of the paper in case you downloaded it. There you should find which kit was used so you can look for the file at the company website.

[maria2019]

I see. I will check it out. Thanks for your response.