Hello!
I am using samtools view to map short reads (-phred33) against a reference genome.
The problem is that I don't know how to properly filter the mappings based on their quality since I'm unsure of how to choose proper value for --min-MQ parameter (that is, the minimum mapping quality).
The reads I intend to map belong to an organism of the same genus but a different species than the organism to which the reference genome belongs. In both species, the rates of heterozygosity and hemizygosity are relatively high, so I believe I need some flexibility when filtering the mappings. I would need to find a quality value that is not too low but also not so restrictive as to discard a large number of valid mappings.
I'm not sure if 20 or 30 would be a good --min-MQ value for this purpose...
May I ask for some help?
Thanks a lot.
I am using samtools view to map short reads (-phred33) against a reference genome.
The problem is that I don't know how to properly filter the mappings based on their quality since I'm unsure of how to choose proper value for --min-MQ parameter (that is, the minimum mapping quality).
The reads I intend to map belong to an organism of the same genus but a different species than the organism to which the reference genome belongs. In both species, the rates of heterozygosity and hemizygosity are relatively high, so I believe I need some flexibility when filtering the mappings. I would need to find a quality value that is not too low but also not so restrictive as to discard a large number of valid mappings.
I'm not sure if 20 or 30 would be a good --min-MQ value for this purpose...
May I ask for some help?
Thanks a lot.
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