dna-seq-gatk-variant-calling

dna-seq-gatk-variant-calling copied to clipboard

VQSR not fully implemented

4

It seems that the VQSR (GATK VariantRecalibrator) step [here](https://github.com/snakemake-workflows/dna-seq-gatk-variant-calling/blob/cffa77a9634801152971448bd41d0687cf765723/workflow/rules/filtering.smk#L29-L39) is not fully implemented. That rule only produces the model built with the [VariantRecalibrator](https://gatk.broadinstitute.org/hc/en-us/articles/360050815872-VariantRecalibrator), but does not use [ApplyVQSR](https://gatk.broadinstitute.org/hc/en-us/articles/360036431392-ApplyVQSR) to actually...

lczech

Running without known-variants

3

Thank you for making these workflows! In many cases I work with samples without previously known variants available. Is it possible to configure this workflow to skip steps that rely...

silastittes

Errors in two rules terminating run

2

Hello, I'm getting the following errors that result in a downstream termination of the pipeline. ``` Error in rule get_genome: jobid: 4 output: resources/genome.fasta log: logs/get-genome.log (check log file(s) for...

CAllex-Buckner

missing python dependency in rule plot_stats

2

I got the following error running this workflow, ``` [Thu Oct 21 10:30:39 2021] rule plot_stats: input: results/tables/calls.tsv.gz output: results/plots/depths.svg, results/plots/allele-freqs.svg log: logs/plot-stats.log jobid: 24 resources: tmpdir=/tmp Activating conda environment:...

pmginacio

Hey everyone, I just had a look at the logs and I realized that `REMOVE_DUPLICATES` is set to false there even though it's set to true in the configs. I...

gernophil

Hey everyone, I'm trying to allocate some more memory to rule recalibrate_base_qualities since it's taking ages. I tried to allocate more memory and threads through the java opts, but the...

gernophil

Choice of reference genome

2

I might have missed the information in the documentation, but I don't think there is a way to input a custom-made reference genome for the alignment step. If I have...

ThibauldMichel

knokknok

Peppy

18

@johanneskoester @nsheff Note that `units_peppy.tsv` is included not for necessity, but to show how a `peppy` user may encode a subsample/units table, and have it still function with the workflow.

vreuter

Not executed fastqc for specified inputs

1

hi. I recently executed this pipeline for my job. But after I ran this pipeline and removed the output of the fastqc, I can't reproduce the output of fastqc (qc/fastqc/A-1.html...

nkimoto