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The existing [SARS-CoV-2 variant analysis] tutorial is focused on the analysis of metagenomic sequencing data. The majority of data being produced, however, uses the ARTIC amplicon protocol (for Illum…
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A user is having an issue when their file paths have spaces in an arguments file. This issue does not exist when there is no arguments file. It would be helpful for GATK to be able to parse shell quot…
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Hello Sir/Ma'am,
1] Trying to apply oncocnv for exome data i.e. without reference to amplicon id. What should be modification required in bed file for applying it on Exome data.
Standard bed …
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Just pulled PAA down the other day and have running it, my run command is:
/data/PrepareAA/docker/run_paa_docker.py -o /data/output -s Colo -t 16 --bam /data/Data/Colo/cofinal.bam --run_AA --run_A…
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Hi Author(s),
I think it is super cool that you've implemented this dynamic strategy!
We where trying to normalize some amplicons on a given chromosome, so we made sequences that where unique to…
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Hello,
I am interested to confirm an allele frequency for a SNV in BRAF gene using amplicon sequencing data. The length of amplicon is 271bp, and paired reads are 101X2. So there is a gap between t…
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Running to an issue with variant assignment of omicron datasets with the ARTIC pipeline reverts variants to the reference despite sufficient read support for the variants in the bam file.
The variant…
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Hi everyone,
I was analysing amplicon reads from 16s V3-V4, using 341F-806R primer set. The quality of the reads are fairly good:
![image](https://github.com/user-attachments/assets/0dcf3987-3bbc-…
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Hello!I have some errors when running the program, I would be grateful if you could take time out of your busy schedule to answer my doubts.Pic 1:Is it because of the primer dimer in the result, an…
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The workflow could be run on all amplicons only (and not specific target SNPs aswell). If we can reduce the number of inputs for some users that's a bonus.
Things like allele frequencies and cover…