pablo-gar/somatic_mutations_gtex

Methods and analysis for Garcia-Nieto, et al. Somatic mutations

somatic_mutations_gtex's Issues

Output not recieved in mappingMutationCalling_pipeline

Hello,

Thank you so much for sharing your code.

I was trying to reiterate your code on my data from GTEx but I am coming on some problems for a while now.

`localrules directive specifies rules that are not present in the Snakefile:
organize_tissues

Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 6
Rules claiming more threads will be scaled down.
Job stats:
job count min threads max threads

---

all 1 1 1
total 1 1 1

Select jobs to execute...

[Wed Jul 6 18:15:53 2022]
localrule all:
jobid: 0
reason: Rules with neither input nor output files are always executed.
resources: tmpdir=/tmp

[Wed Jul 6 18:15:53 2022]
Finished job 0.
1 of 1 steps (100%) done
Complete log: .snakemake/log/2022-07-06T181548.389176.snakemake.log`

However, there is no error from this but there is no output at the same time as well.
Please guide me.

GTF_gtex_exonBoundaries file

somatic_mutations_GTEx/mutationCalling/Snakefile

Hello,

I would like to thak you for uploading your code to github, it is very helpful. I am trying to adapt your pipeline to my data for my PhD, especially for the filtering steps of the mutations. In your script somatic_mutations_GTEx/mutationCalling/Snakefile, you use a file GTF_gtex_exonBoundaries. I was wondering how it was created. I am working on hg38 and I would like to update my annotation file so it works in your pipeline.

Thanks,

Pauline

How to generate Panel of Normals for the pipeline?

Hello,

I would like to use the pipeline to call somatic mutations from tumor-only RNAseq data. Would you mind to detail that how to generate the Panel of Normals?

Thanks,
Ya

what is an "PileupPartitionSize"?

Dear, @pablo-gar

I am trying to run this pipeline in hg38, but couldn't figure out some of the input files.
Inside the mappingMutationCalling_pipeline/SnakefileFastaqPrep.smk, what should I use for "pileupPartitonSize"?
When I look up the config file, the only thing I find regarding "pileupPartitonSize" is
which I think isn't the right input.

Also, where can I find "GTEx_Analysis_2016-01-15_v7_WholeGenomeSeq_652Ind_GATK_HaplotypeCaller.vcf.gz"?
If I have difficulty finding this file, will it be okay to use dnSNP or gnomAD instead?

Would really appreciate your advice.
Thanks
Jen