Annotation and variant calling on diploid systems

Hi. I need help with SAM files. I have a SAM file but i dont have idea how to view the result to finds snp, coverage, etc. is there any program to view and interpret easier? thanks

Hi @Dardo_Dallachiesa,
what is the purpose of your analysis? SAM files store information about sequence alignment against a reference, but it doesn’t include explicit information about SNPs or coverage.

Regards

Hi Gallardo. Thanks for the answer. I have phaseolus vulgaris genome with the genes and the phaseolus lunatus only with the raw sequence and I downloaded the reads. I want to see if some genes of vulgaris are in lunatus (like nfr1, nfr5) and be able to make the annotation. The propouse is discover variation, snps. Sorry if i dont be clear I m new in bioinformatics.

Regards

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Hi @Dardo_Dallachiesa,

in that case, I suggest you have a look at these two trainings:

however, I found that the genome of P. lunatus have been annotated already: annotation. Perhaps it can be useful for you.

Let me know if you have any additional questions as you begin the analysis.

Regards

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