-
@gregorgorjanc @RosCraddock
Originally, while estimating the alternative allele frequency of the whole population, the algorithm looped over the genotypes of all the individuals to calculate the most…
-
Hi
I have simulated some haploid data with Illumina error rates and ancient DNA data. It is ~25x coverage.
I wanted to see how the damage influences heterozygosity/genotype calls.
I noticed that …
-
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…
-
In Population Frequencies tab in the variant browser the genotype frequencies are NaN for UK10K and Gnomad
-
[VariantContextUtils](https://github.com/samtools/htsjdk/blob/master/src/main/java/htsjdk/variant/variantcontext/VariantContextUtils.java) currently calculates allele frequencies using AC/AN, but thes…
-
Hello,
I successfully ran est_p, and am now trying to estimate the hybrid index using default settings. The data for the putative hybrids is formatted the same way as the parentals, but I am gettin…
-
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
2 months ago
-
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…
-
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…