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I am using CNVkit to call somatic CNAs from tumor-normal paired WES data. The BAM files were generated using GATK pipeline and the somatic VCF file was called using Mutect2 pipeline. However, I am get…
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Hi Ryan,
I've read your posts on using SVTyper to help with somatic variant filtering. You suggested only keeping variants that have a non-reference genotype in the tumor (GT != 0/0) and variants t…
mej54 updated
6 years ago
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From Noor Dawany
> I just wanted to bring to your attention that the CHOP cohort frequencies reported in Varify do not follow the conventional equation (from population genetics) for calculating alle…
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This is the summary of the desired behavior @pnrobinson needs to proceed with using WebPhenote effectively for curation.
The current plan is to enable Peter to import an existing TSV, edit and exte…
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Hello, I'm revisiting this comment as I've run into a similar observation in my dataset- the FS field (fisher test for strand bias) does not seem to be correctly populated — it is coming up as zero fo…
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I've been running Clair3 (v1.01) on some pig samples with ONT reads. I noticed that Clair3 has been assigning the "1/1" genotype to SNVs that have an allele frequency where I would expect an "0/1" gen…
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How may I solve this?
$ python gwas_summary_imputation.py -by_region_file $DATA/eur_ld.bed.gz -gwas_file harmonized.test.txt.gz -parquet_genotype $DATA/reference_panel_1000G/chr1.variants.parquet…
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スラッシュやカッコやID以外の文字列の意味を確認し、MOLECULAR_DATAを適切なデータセットに紐づける
```
%ruby bin/split_moleculardata_each_dataset_from_humandb_both.json.rb json_from_joomla/humandb_20231223_both.json |grep hum0014 |jq -r '.…
tfuji updated
3 months ago
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As suggested by a reviewer, it'd provide helpful context to say what sort of data was used to fit the demographic models, so users can guess how what aspects of the data simulations are expected to re…
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Hi - wanted to revisit this and see if it's still a problem with recent versions of bcftools. Quickly scanning my data, it does not appear to be, but wanted to get confirmation.
From @lh3 on https:/…