I have a exome sequencing data of parents and their child. We are trying to identify the candidate genes responsible for some abnormality.I have never used CLC genomics workbench.
Do I need a licensed version for the trio analysis ?
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.
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