Is it possible to map the Miseq data to the reference?

Question

[Cherry]

Hi, everyone, I would like to know some info about SNPs in one species but only MiSeq data is available. So my question is: Is it possible to map MiSeq data to a reference using mapping software (e.g. bwa or stampy) and then call SNPs using GATK?

Any suggestion would be appreciated! Thanks in advance.

[dariober]

Actually, I would say that it is not only possible but also recommendable. Among the NGS sequencers I think the MiSeq is the one that gives the highest base quality with pretty long reads like ~300bp (long for Illumina standard at least.). Then of course, for large genomes the throughput is not high enough.

[Cherry]

It is quite expensive. Usually, it is used only for de novo, I guess.

Answer 1

[Devon Ryan]

Sure, using bwa mem and then GATK is a popular pipeline for this sort of task.

[Cherry]

Hi, Devon, Thanks for your quick replay! I will try it!

Answer 2

[Evgeniia Golovina]

Or, you can use bwa + samtools mpileup pipeline as the alternative.

[Cherry]

Thanks, Jn.Golovina.