Deleted:Exctracting amino acid substitutions

Question

[nermze86]

Good day,

I'm trying to develop a pipeline to determine mutations which are responsible for amino acid changes in genes associated with antibiotic resistance. I have roughly 300 bacrtial isolates.

My approach so far has not been fruitful, in short this is what i tried:

1. Map all my fastq sequences individually to a gene using BWA.
2. Converted output SAM to BAM, subsequently sorted all BAM files.
3. Run FreeBayes in order to get a vcf file with SNP's
4. Run VCF-annotator to get the amino acid change from the vcf file

My approach is probably flawed, but at this point I'm out of ideas. The results i get at the end are wrong.

Any help/input how I should approach this issue is greatly appriciated.