Damilola Oresegun

VCF output not reporting translocations/inversions/duplications

2

Hi, I have used the command below to carry out a variant call with nanopore reads. `snakemake --snakefile /home/doresegu/scratch/apps/Tools/pipeline-structural-variation-2.0.2/Snakefile -p call --config input_fastq=/home/doresegu/scratch/private/Analysis/IsolatesToAssemble/sks047.fastq reference_fasta=/home/doresegu/scratch/private/PublicationAnal/NewGenomes/Cultured.fasta sample_name=sks047VsCultChecks --cores 32` This worked great...

This adds an update to the kreport2mpa.py script to allow the generation of an output report that is compliant with metaphlan version3. Changes to the original script are clearly labelled....