How To Get The Genotype From Sequence Data?

Question

[Stingery]

I have a data set of unphased sequence data, i.e. one nucleotide sequence per locus per individual. From there, I would like to compute the genotype, because a wide range of statistical software works with the genotype, but not the sequence. How can I do that? Is there a programme, which I could employ?

Thanks!

Answer 1

[Giovanni M Dall'Olio]

You have to do a type of analysis called SNP calling. There are many tools to do it, depending on the type of data you have. A good starting point may be bowtie used in combination with samtools; have a look at its tutorial, it should be a good primer. Another tool is gatk.

Have also a look at the other discussions in this website. For example:

• what is SNP calling?
• SNP calling tools and costs

Answer 2

[Khader Shameer]

If you have a VCF file after QC, Alignment/Mapping and Variant calling steps you can get the genotype data from it (using utility or use vcftools to filter based on various conditions (Read about VCF specifications here and VCFtools manuscript here) . If you have any missing genotypes, you can perform genotype imputation. If you are new to analysis of NGS data refer to Giovanni's answer and other sequencing related discussions at BioStar.

[Giovanni M Dall'Olio]

+1 for the nice answer and for the new photo plus hair cut! :-)

[Khader Shameer]

Thanks Giovanni :) !