variants with low coverage.

[iolanda-IZSAM]

Dear Torsten,

we use snippy in order to align the reads to a reference and to obtain the annotation of the variants. Unfortunately in the results that we obtain we loose some SNPs because of the coverage. Snippy replaced the information in the reads with the reference nucleotides. And also in the vcf file we don't have those variation annotated (and for covid it is really important!)

If we extract the consensus using another method (e.g. ivar setting a low min coverage) we obtain the nucleotides present in the alignment

Is it possible to change the min coverage used in snippy?

Thank a lot for your help Iolanda

[maxbranger]

Hello, you can use --mincov (default is 10) M.

[andersgs]

Thank @maxbranger. @iolanda-IZSAM there are two other options you may want to be aware of, and wish to experiment with: https://github.com/tseemann/snippy#the-variant-caller

Keep in mind that Snippy does not account for the incorporation of primer into amplicons like iVar does. That could lead to erroneous SNP calls if you are using tiled amplicon seq.

Best of luck.

[andersgs]

I am closing the issue. Please reopen if necessary.