koelling / amplimap Goto Github PK

documentation here: https://amplimap.readthedocs.io/en/v0.4.8/configuration.html

Targets are checked for overlaps before running pileups, but this can happen after much of the pipeline has already run. It would be good to check this before starting.

However, we should only do this if pileups/pileup_snps is one of the targets because for variants/coverages we actually auto-merge overlapping targets together. It will be hard to do this properly though, since pileups may be called indirectly through other rules.

So either disallow overlapping targets for variants/coverages too, or always auto-merge? Or make it an option?

It would be useful to have a script that can generate plots based on the pileups, similar to the plot in the supplementary figure here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5638069/

Probably best to implement this as a separate R script rather than making this part of the pipeline. Otherwise we'll have to add R as a requirement.

Hi, the link for the FASTQ files of the FGFR2 tutorial seems broken, could you fix it please?

wget http://userweb.molbiol.ox.ac.uk/public/koelling/amplimap/tutorial_data/FGFR2.tar

--2023-06-07 09:39:03-- http://userweb.molbiol.ox.ac.uk/public/koelling/amplimap/tutorial_data/FGFR2.tar
Résolution de userweb.molbiol.ox.ac.uk (userweb.molbiol.ox.ac.uk)… 163.1.16.78
Connexion à userweb.molbiol.ox.ac.uk (userweb.molbiol.ox.ac.uk)|163.1.16.78|:80… connecté.
requête HTTP transmise, en attente de la réponse… 301 Moved Permanently
Emplacement : https://userweb.molbiol.ox.ac.uk/public/koelling/amplimap/tutorial_data/FGFR2.tar [suivant]
--2023-06-07 09:39:04-- https://userweb.molbiol.ox.ac.uk/public/koelling/amplimap/tutorial_data/FGFR2.tar
Connexion à userweb.molbiol.ox.ac.uk (userweb.molbiol.ox.ac.uk)|163.1.16.78|:443… connecté.
Erreur : impossible de vérifier l'attribut userweb.molbiol.ox.ac.uk du certificat, émis par «CN=R3,O=Let's Encrypt,C=US» :
Le certificat émis a expiré.
Pour établir une connexion non sécurisée à userweb.molbiol.ox.ac.uk, utilisez « --no-check-certificate ».

Hello,
I was trying to complete the variants_umi rule but always get an error mesage which causes amplimap to exit the analysis.
Error:

Error in rule annotate_variants:
jobid: 0
output: analysis/variants_umi/SAMPLE1.vcf.normalized.vcf.gz.hg19_multianno.csv, analysis/variants_umi/SAMPLE1_S16.for_annovar.bed
RuleException:
CalledProcessError in line 1581 of /mnt/tools/miniconda/envs/amplimap/lib/python3.6/site-packages/amplimap/Snakefile:
Command 'set -euo pipefail; convert2annovar.pl analysis/variants_umi/SAMPLE1_S16.vcf.normalized.vcf.gz -format vcf4old --includeinfo > analysis/variants_umi/SAMPLE1_S16.for_annovar.bed;
table_annovar.pl analysis/variants_umi/SAMPLE1_S16.for_annovar.bed "/share/user/Reference_Genomes/annovar/humandb" --buildver "hg19" --otherinfo -csvout -remove -protocol 'refGene,esp6500siv2_all,1000g2014oct_all,avsnp147,cosmic94_coding, cosmic94_noncoding,dbnsfp33a,clinvar_20150629,dbscsnv11,exac03,gnomad_genome,gnomad_exome' -operation g,f,f,f,f,f,f,f,f,f,f,f --outfile analysis/variants_umi/SAMPLE1_S16.vcf.normalized.vcf.gz ;' returned non-zero exit status 2.
File "/mnt/tools/miniconda/envs/amplimap/lib/python3.6/site-packages/amplimap/Snakefile", line 1581, in __rule_annotate_variants
File "/mnt/tools/miniconda/envs/amplimap/lib/python3.6/concurrent/futures/thread.py", line 56, in run
Exiting because a job execution failed. Look above for error message

if I call the table_annovar.pl command with the given options it does run without an error and puts out an csv file.

I'm using Amplimap version 0.4.20
and annovar 2019Oct24

Has anybody had this behaviour before?
Thanks in advance!

Hi, we designed the backbone sequence of smMIP by ourself, I'd want to know the format of the design.csv, could you please give me an example? Thanks a lot.

Trying to download the fastq files from the tutorials (in order to check installation), but getting an error.

$ wget http://userweb.molbiol.ox.ac.uk/public/koelling/amplimap/tutorial_data/TLK2.tar

--2022-04-19 14:21:08-- http://userweb.molbiol.ox.ac.uk/public/koelling/amplimap/tutorial_data/TLK2.tar Resolving userweb.molbiol.ox.ac.uk (userweb.molbiol.ox.ac.uk)... 163.1.16.66 Connecting to userweb.molbiol.ox.ac.uk (userweb.molbiol.ox.ac.uk)|163.1.16.66|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://userweb.molbiol.ox.ac.uk/public/koelling/amplimap/tutorial_data/TLK2.tar [following] --2022-04-19 14:21:09-- https://userweb.molbiol.ox.ac.uk/public/koelling/amplimap/tutorial_data/TLK2.tar Connecting to userweb.molbiol.ox.ac.uk (userweb.molbiol.ox.ac.uk)|163.1.16.66|:443... connected. HTTP request sent, awaiting response... 404 Not Found 2022-04-19 14:21:10 ERROR 404: Not Found.

Any other locations to download this data?

Thanks in advance