atlas/docs/usage/genotyping.md

[hcdenbakker]

Tried my first atlas genotyping, tried the genotype gene panel example: atlas genotype :sample sample_*.fastq.gz gn-amr-genes.fasta.gz This did not work, gave me the following error: atlas: error: unrecognized arguments: sample_2.fastq.gz gn-amr-genes.fasta.gz

I ran into multiple errors, but in the end I got it to work with the following command line: atlas genotype --seq sample_*.fastq.gz --mccortex31_path /home/henk/atlas/mccortex/bin/mccortex31 sample gn-amr-genes.fasta.gz

Do the docs need updating, or is this something related to my system?

[Phelimb]

Hi @hcdenbakker,

I think this is down to poor documentation - sorry!

sample_*fastq.gz should be the path to your fastq and the gn-amr-genes.fasta.gz should be a path to the file.

For example, if we're in the atlas dir something like this should work by replacing the fastq path to one of your fastq:

atlas genotype C00007012 mykatlas/data/gn-amr-genes.fasta.gz --seq /data2/users/phelim/data/gn/atlas/fastqs/C00007012.fastq.gz --mccortex31_path /home/henk/atlas/mccortex/bin/mccortex31

[hcdenbakker]

Thanks Phelim, Makes perfect sense, I am just trying to figure out what I can/can't do with atlas and it is probably a little bit premature to update the docs at this stage of development.

[Phelimb]

No problem @hcdenbakker. Let me know if you have any questions about what can be done. You can create your own panels for genotyping if required.