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Hi, Wei
I tried both GATE v0.45 and 0.44 docker image for survival analysis on UKB RAP platform. The first step looks good, and I got result, but for the second step, with the following setting,
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Analyze.cosmic_fit(samples='/autofs/bal34/okwong/cancer_stat_proj/SigProfiler/lab_data',
output="/autofs/bal34/okwong/cancer_stat_proj/SigProfiler/lab_data/lab_data_test_GRCh37_100…
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Hello,
I have noticed that some of my outputs do not create a consensus or haplotype fasta file. I wanted to make sure I understood the issue so I looked at the `rvhaplo.sh` script and captured the…
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In this [example](https://github.com/uclahs-cds/package-iSubGen?tab=readme-ov-file#load-and-format-data), `csnvs` should be `snv`
In this [example](https://github.com/uclahs-cds/package-iSubGen?tab…
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I have installed remixt and started downloading the reference data, but that process failed with message
--2023-10-11 06:02:33-- http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1…
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When I was running ScanNeo2, several samples encountered errors during the VEP annotation process, specifically for the main task of SNVs. The following error occurred for all of them.
localrule ann…
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### Description of feature
I have data consisting of several unrelated trios and several individuals. Is it possible to run the pipeline with just one samplesheet (where cases have different case_id)…
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I am looking to have both SNV called and non SNV's in the same vcf for downstream analyses.
My temporary workaround at the moment is to run the tool twice, once with the reference to generate the …
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Hello,
I'm new to Palimpsest and I'm trying to preprocess and annotate input data but I have an error that I don't understand. I tried with other data and it worked. Any suggestion ?
![session i…
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**Is your feature request related to a problem in the current program to new available techology or software? Please describe and add links/citations if appropriate.**
Our local geneticists are loo…