In order to rerun my analysis from the exome pipeline I decided to try different experiments in order to evaluate which one fits better my analysis. So far I came up with this ideas:
Experiment 1
Use Fastx toolkit to clean the reads, align with BWA, postprocess with GATK and evaluate the genotype of the individual
Experiment 2
Use Trimreads to clean the reads, align with BWA, postprocess with GATK and evaluate the genotype of the individual
Experiment 3
Do no trimming, align with BWA, postprocess with GATK and evaluate the genotype of the individual
Experiment 4
Use SOAP to align and call SNPs
I’m planning to use one individual from 1000 genomes to compare the genotype.