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Looks good. Unrelated to this PR but I think the stats files should go to the `QC` directory
```
/hot/software/pipeline/pipeline-call-gSV/Nextflow/development/unreleased/mmootor-replace-d…
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I'm trying simple cwl script below name `vcfstat.cwl`
```
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class CommandLineTool
baseCommand: bcftools stats
inputs:
vcf_file:
type: File
…
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I am getting the following error when running vcfstats and I do not know how I can go about this error. Can someone help with this:
```bash
vcfstats --vcf output_filtered.vcf --outdir examples/ -…
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e.g.
```
rule generic_vcf_stats:
input:
vcf = Path('{folder}', '{file}.vcf.gz'),
tbi = Path('{folder}', '{file}.vcf.gz.tbi')
wildcard_constraints:
folder = 'ou…
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Figure 1: Training & Testing Data
A.
Pipeline Schematic for identifying truth variant set
B.
Comparison of CG with Illumina Phased Pedigree results for NA12877 vs GIAB NA12877
just …
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improve pipeline to automatically filter and create `.maf`
1. add vcf2maf to docker:
```
conda install -qy -c conda-forge -c bioconda -c defaults ensembl-vep==101.0 htslib==1.10.2 bcftools==1.1…
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Sample level quality control data (FastQC, Flagstat, Vcfstats) is stored in CloudSQL database tables. It's not easy to trace the provenance of data from GCS -> CloudSQL right now. Also, not easy to kn…
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Trellis uses a Neo4j database to store metadata related to data objects and jobs. Data generated from quality control procedures such as FastQC, Flagstat, and Vcfstats are stored in a Postgres relatio…
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Hello @yunfeiguo
I'm trying to replicate the generation of fastqs using varsim_multi.py and i keep getting stuck towards the end:
here is the command i used:
`python /Public/varsim/master/va…
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### Operating System
CentOS 7
### Other Linux
_No response_
### Workflow Version
v2.2.0
### Workflow Execution
Command line (Cluster)
### Other workflow execution
_No response_
### EPI2ME Ve…