Feature add af to vc fs

[MarieLataretu]

• outputs an additional VCF with the alternate allele ratios (AF) for all passed and failed variants
• only for ARTIC w/ medaka and fast5 or fastq intput
• adds a column to the datatable (tsv and excel) containing the number of mixed sites of the sample
  • definition of a mixed site: INFO/DP>${params.min_depth} & INFO/AF>=0.3 & INFO/AF<=0.8

Relates to/fixes (?) #266

All three test profiles run successfully:

nextflow run poreCov.nf -profile test_fast5,slurm,singularity --cachedir [...] -resume --update
nextflow run poreCov.nf -profile test_fastq,slurm,singularity --cachedir [...] -resume --update
nextflow run poreCov.nf -profile test_fasta,slurm,singularity --cachedir [...] -resume --update

[hoelzer]

oh wow - so it is actually possible to get allele frequencies (AF) from medaka? This would be really nice to have... thx

[MarieLataretu]

It's "stolen" form Galaxy 😅 [MIT license, so all good]

After ARTIC they do the following:
medaka tools annotate --dpsp --pad 25 and then a custom python script that does things and adds a AF INFO field

I can't say how it compares to other tools, but it's seems to be somewhat in line with what one would see in IGV.

[hoelzer]

Nice!

[replikation]

we do some quick test runs and merge when fine. thank you :)

[replikation]

works on our end