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## This section is required for PM/ADAPT team
### [Required] For what study (study_id) is this request?
### [Required] Basic study information
- [ ] Is this an OT or Kids First study…
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Good morning,
I have tried converting my file from vcf to maf with a line
perl vcf2maf.pl --input-vcf /media/milda/Elements/OneDrive/OneDrive/TXT_files/COADandREAD/VCF_files/COAD.vcf/COAD_CYT-High…
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The following rule `delly_cnv_tumor_normal` fails to run due to missing bcftools in the delly container
https://github.com/Clinical-Genomics/BALSAMIC/blob/e3cc0ce2f27c3056d135caabeae22b8401f0abb1/…
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I am using infercnv using `NULL` as the reference on a single sample. I have tried to change my code several ways (i.e. setting `analysis_mode="subclusters"` and also using the default setting for th…
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The code linked below is used to derive Table 1 in the manuscript, but this code double counts samples where there are WGS and RNA-seq biospecimens.
https://github.com/AlexsLemonade/OpenPBTA-analy…
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https://mp.weixin.qq.com/s/UEighpXB38yRQ3AWv8vKrg
ixxmu updated
2 years ago
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**Is your feature request related to a problem? Please describe.**
The idea is to generate a PON reference using all the normal blood samples from the GMCKsolid panel that was sequenced earlier here …
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The current `varcall_py27` develop container has issues while running manta. Missing the script
```bash: line 7: /opt/conda/share/manta-1.6.0-1/libexec/convertInversion.py: No such file or directo…
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https://mp.weixin.qq.com/s/7NbSp9UZVRUK3F1YqZVkWQ
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https://mp.weixin.qq.com/s/-UjKxtszsH7HxRe3Rjh7zg