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Thanks for your great work.
I have been testing this tool the last couple of days and wondering if there are optimal sites to select /subset for the input vcf ?
A large vcf would require lots of mem…
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### Description of feature
`spliceai_21_scores_raw_snv_-v1.3-.vcf.gz` contains scores for chr21, and not those overlapping the testdata.
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Hello,
I am attempting to use MMARGE for analyzing ATAC-seq data from different strains of mice. I downloaded the SNP and Indel vcf files from the Mouse Genomes Project website and sorted them usin…
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Hello Nikolaos and Pavlos,
I understand there were issues about Mahattan plots already asked by other ppl. However, I am encoutering something new that others did not mention. I am hoping to get som…
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## **Is your feature request related to a problem? Please describe.**
See #1581 for how this feature request started or other context.
Others:
https://github.com/snakemake/snakemake/issues/917
h…
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**Description:**
Add subcommands for generating only exclusion or inclusion BED files without running the full pipeline. Possible subcommands:
- `generate-exclusion-bed`
- `generate-inclusion-bed`
…
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Hello Fritz & SURVIVOR dev team,
### What.
I attempted to use the VCF file generated by SURVIVOR with _bcftools_, as for instance recommended in issue https://github.com/fritzsedlazeck/SURVIVOR/i…
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**Is your feature request related to a problem? Please describe.**
VCF preprocessing, currently done by bcftools, requires `##FILTER`, `##FORMAT`, `##INFO`, and `##contig`, which is too strict.
…
arine updated
2 months ago
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Hi,
I'm using SURVIVOR (v1.0.7) for the first time and trying out some test data.
I've generated a params file using
`SURVIVOR simSV test_params.param`
and then simulated the SVs onto a reference…
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**Describe the bug**
When trying to simulate desired insertions from VCF file, the insertions are not present in the resulting reads. Golden VCF file is completely empty after successful run (no muta…