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.

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