Hello, In my tblastn results, I only want results with a minimum percent coverage of 66. I found -qcov_hsp_perc but it's for hsp, not for the subject. -qcovs option doesn't function for tblastn and I can't find any other option. Do you have any idea which option to add?
No, there is no such option I'm afraid.
moreover, it would not make sense to have this covs parameter in relation to the hit as tblastn is a blast of a protein against a nucleotide DB which in most cases will be genomic sequences of which only small part of it will be matched by the protein.
Best you can do is implement something yourself , based on the tab output format that should be doable.
the qcovs is an output field you can request for the tabular output, it is not an option you can provide on the cmdline (not only for tblastn, for all the blast flavours btw)
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version 2.3.6
OK thanks for your answer !