Is it possible to map the Miseq data to the reference?
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.
2 answers
Sure, using bwa mem and then GATK is a popular pipeline for this sort of task.
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Devon Ryan
Or, you can use bwa + samtools mpileup pipeline as the alternative.
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Evgeniia Golovina
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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.
It is quite expensive. Usually, it is used only for de novo, I guess.