I recommend to use open source tools for exome sequencing data like bowtie,bwa-mem, freebayes,gatk,etc. 

I recommend to use open source tools for exome sequencing data like bowtie,bwa-mem, freebayes,gatk,etc. 

As Rahul mentions, every step you need for trio analysis can be done using open-source tools:

The steps involved usually look something like:

1) Alignment of raw (FASTQ) data: e.g. bwa-mem (http://bio-bwa.sourceforge.net/)

2) Mark Duplicates: picard (http://broadinstitute.github.io/picard/)

3) Quality Score recalibration GATK (https://www.broadinstitute.org/gatk/)

4) SNP-calling (GATK Haplotype-Caller) (https://www.broadinstitute.org/gatk/)

5) Annotation of SNPs (which gene is involved, how common is that variation...): annovar (http://www.openbioinformatics.org/annovar/)

It might be a bit tricky to get all of those applications running, but they are all well-documented and a somewhat computer-literate person will be able to do that.

Unfortunately, I can't give any advice for CLC Bio, since I never used it.

Another option might be Galaxy (https://usegalaxy.org/) You should in theory be able to run most of the analyses there...

Thank you Rahul and Peter. I will try working on these.