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in particular for collecthsmetrics since it has higher coverage cap metrics available, but should consider upgrading for all processes/metrics that are obtained via picard tools. this could potentiall…
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Hi,
I'm trying to phase rare variants, which goes well for the greatest part. I used the files and instructions you provided in the [documentation](https://odelaneau.github.io/shapeit5/docs/tutoria…
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we use it in exome, in the filter_vcf step, but the gnomad vcf we're using is only a subset, restricted to exome coords. Would be nice to revisit that decision at some point (options: leave it out, a…
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Replicate the Germline Exome & HLA typing stepwise on AWS and record documentation on Google doc.
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In case we dont have > 30 exomes, we could simply set up the VQSR recalibration step to take 30 exome samples from 1000G and use these as calibration samples. For bigger clusters, we could even store …
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**Is your feature request related to a problem? Please describe.**
When rules are run through a wrapper it is difficult to see which command is actually being run, since the commands are not printed …
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@mandichen
Hi,mandichen
Good job and I am very interested in your research, but I have some questions.I used the sample data BM2_v0s0_n_200.h5ad and Macosko_cell_cycle_genes.txt to get the follow…
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I am trying to demultiplex tumor samples using genotype data from healthy cells, and demuxlet is calling the majority of my tumor cells doublets. I'm looking for any insight about whether somatic muta…
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I'm using this script:
```
#!/bin/bash
# Parameters to replace:
# The GOOGLE_CLOUD_PROJECT is the project that contains your BigQuery dataset.
GOOGLE_CLOUD_PROJECT=psjh-eacri-data
INPUT_PATTER…
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**Snakemake version**
5.15
**Describe the bug**
I'm able to trigger a bug with an undefined variable.
**Logs**
```
Traceback (most recent call last):
File "/fast/projects/medgen_resea…