Mutserve annotate output interpretation

Question

[nihilior]

Hi everyone,

I am using Mutserve for calling and annotating mitochondrial variants. I get a textual output with a number of column fields. Does anybody know where I can find a detailed description of all the fields? I checked the Mitoverse documentation but I can not find a proper description. Thanks in advance

Answer 1

[thach]

I used it also. You can see the result in VCF format which is described here https://samtools.github.io/hts-specs/VCFv4.2.pdf Important info are GT:AF:DP which are Genotype, Allele freq, sequence deep.

[nihilior]

Thanks thach for the response. Of course they are important informations of the vcf file, but Mutserve also outputs a txt file, which is then annotated by Mutserve Annotate. In such file, there are fields like: Maplocus, OXPHOS_complex, NuMTs_dayama, DuplSeq_rCRS and many others. Do you know any resource from which one can retrieve information about those fields? Thanks

Answer 2

[thach]

Which version did you use? I used up to date version v2.0.0-rc13 and only has these fields in.txt file ID Filter Pos Ref Variant VariantLevel MajorBase MajorLevel MinorBase MinorLevel Coverage CoverageFWD CoverageREV Type

[nihilior]

I used the same v2.0.0-rc13 version. The fields that you list come from Mutserve call. The next step (Mutserve annotate) adds basic annotation to the Mutserve call output from the "rCRS_annotation_2020_08-20.txt" file, which contains additional fields, such the ones I listed before.

Answer 3

[thach]

I think the field you mention are precomputed and annotated from reference mt genome. It is not the output. I guess they have define some mutation hotspot there

Answer 4

[nihilior]

Found the fields! Don't know how I did not found them in the first place: https://github.com/seppinho/mutserve/blob/master/files/rCRS_annotation_descriptions.md