Hello
I am trying to call indels using human exome sequence using Freebayes as well as Lofreq tools but I could find indels in output vcfs.
Any advice and comment.
Regards
Kamran
Welcome @kamran.azim
The first item I would check is the reference data involved. Both the choice used with Freebayes and the version of the reference assembly used to generate the VCF files. Variant calling is comparing base-to-base differences. If the coordinates are “off”, no valid scientific calls is a common symptom.
If you are working at UseGalaxy.org, this is more about the human assembly version hosted on the server natively → Reference genomes at public Galaxy servers: GRCh38/hg38 example
That guide includes some help for reviewing assembly choices from other sources, including custom genomes, and you are welcome to ask questions!
Comparing to the tutorials can also help. Find these linked from the bottom of the tool forms. Just keep in mind that these simple examples may use mostly defaults settings while read world data may need more customization. But I wouldn’t expect zero calls from only poor settings with full sized human samples – which is why I am suggesting that you examine the technical process data/steps itself first.
Please review and if you want to share examples of where you are now we may be able to offer more specific suggestions.
Let’s start there, thanks! 