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Hi, Tanya. Can you please prepare a table that lists…
+ [x] the number of GitHub watchers, stars, and forks for each formula in Homebrew/science that has a GitHub a repo https://github.com/Linuxbre…
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## Describe the issue
I used the t2t cache file provided in "https://ftp.ensembl.org/pub/rapid-release/species/Homo_sapiens/GCA_009914755.4/ensembl/variation/2022_08/indexed_vep_cache/"; However, the…
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Hi, I have vcf data pool sequencing generated from VarScan that seems not compatible with your -p option in Dsuite Dtrios. An error message of the AD field not found or something. Would you mind send …
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recipe | lints
----------------------|----------------------
recipes/2pg_cartesian | ['missing_license']
recipes/advntr | ['should_be_noarch']
recipes/aenum | ['in_other_channels'…
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It seems that currently I can't configure these values in my YAML?
Tumor VAF cutoff applied to individual variant caller results (mutect and strelka) prior to creating a merged VCF
https://github.…
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We need to determine what the specific Python dependencies are for this package.
@jjriley1 has provided the following from a Conda environment they inherited that works but this includes a bunch of
s…
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Hi, we are having trouble getting results out of the Unfixed pipeline. One problem seems to be that the Perl script format_trans.pl returns an empty file.
As I understand the PPE file is created from…
weiju updated
10 months ago
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Hello!
I'm trying to train the AI model with different inputs such as WGS, TITRATION, SYNTHETIC and FFPE. Im running SomaticSeq on a slurm cluster with singularity wherever possible.
I have had ma…
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To improve variant calling efficiency the genome is split up into chromosomes and scaffolds. Then variant calling takes place for each region (chromosome or scaffold) separately. The scaffolds for the…
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This is the VCF that is produced after we remove regions near INDELS. Try converting with the initial VCF that VarScan produces. This is not a big issue because grenedalf can already convert BAM files…