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Dear Ha X. Dang,
Hello, I am trying to analyze clonal evolution using PyClone and ClonEvol.
I have two WES samples from one patient.
When I followed the manual, I could not infer clonal model…
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3.1.7版本
android.graphics.Canvas.throwIfCannotDraw (Canvas.java:1282)
android.view.GLES20Canvas.drawBitmap (GLES20Canvas.java:593)
com.tmall.wireless.vaf.virtualview.view.image.c.b (VirtualImage.j…
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Since variant allele frequency (VAF), allele depth (AD), depth (DP) is the fundamental information to interpret NGS data, but unfortunately it is not readily available in the outputs from Strelka.
If…
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Hello,
I get the following error when running generateFishplotInputs(). Can you please help me fix this? I have attached the input data.txt file for your reference.
f = generateFishplotInputs(resu…
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Hi，
I am using Pindel to call indels in our samples, Our samples are tumor-normal samples, and it's target sequencing data, the library was constructed by capturing.
I used BWA mem to map the tr…
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Getting the following error when trying to estimate `median_vaf_purity` on a combined/merged VCF file.
```python
/home/jacquelineburos/projects/cohorts/cohorts/functions.py in grab_vaf(variant)
…
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Hi Adam,
I'm trying to insert an SNP in a BAM file (30.000X coverage), using the following input:
`chr17 7674230 7674230 1 T`
With REF=C and hg=hg38.
As you can see from the log it takes the…
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python /home/kpadmin/biosoft/TMB/bin/pyTMB.py -i /home/kpadmin/TMB/LST_norm.vcf --effGenomeSize 33280000 --dbConfig /home/kpadmin/biosoft/TMB/config/snpeff.yml --varConfig /home/kpadmin/biosoft/TMB/co…
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Currently we detect mutations at frequencies as low as 5% and rescue hotspot mutations as low as 2%. We should also be rescuing mutations that are `Likely Oncogenic`, `Predicted Oncogenic` and `Oncoge…
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Hello,
When I run infer.clonal.models, an error occurred.
y = infer.clonal.models(variants = data,
cluster.col.name = 'cluster',
vaf.col.names = vaf.col.names,
ccf.col.names = ccf.c…