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Hello Team,
I am trying to use PureCN with a matched tumor and normal samples, however, it's throwing an error. I am attaching the log file here. I have used CNVkit for segmentation and Mutect2 (G…
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Hello,
I am trying to filter vcf files by maf frequency filter in which I only keep SNPs with an MAF>0.01. Below is the command that I ran, however when I look at the output there are still variants p…
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Hi again.
This issue can be merged with #5.
I've used GLIMPSE to impute two samples, and resulted with the following vcf file:
```
(base) batel:~/glimpse/Levant_BA$ bcftools view merged.vcf.gz …
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Hi,
After using gvcfgenotyper on the results of strelka (last version), in the flag filter I find only "." I cannot find for example, the PASS and the other criteria... knowing that in the gvcf of ea…
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> If you wanted to improve confidence further you could supply a somatic SNV vcf to PURPLE. We use Strelka for this, but it should work as long as your vcf contains the AD field which most do.
You …
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Hi,
Thanks for this wonderful tool! I saw there is a Read-aware phasing mode in Shapeit with a read-based phasing script and import the read phasing results to the statistical phasing analysis: htt…
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My first real run for ldweaver on 24 genomes
installed in WSL2Ubuntu
ran the sample set with no problems
did alignments with snippy-multi, verified.
commands at R prompt
library(LDWeaver)
setwd(…
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**Describe the issue**
build PON from multiples samples, all samples are males
**To Reproduce**
Rscript $PURECN/Coverage.R --out-dir $OUTPUTS/normals --bam normals.list --intervals $OUT_REF/hg38_…
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`01-annotate_variants_CAVATICA_input.R` and `01-annotate_variants_custom_input.R` should be modified so that multianno, intervar, and autopvs1 files are filtered to only include variants in vcf file. …
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I'm unsure if this is the case. I'll try to explain as best I can here. So I'm writing a pipeline to do QC of exome data which consist of steps for left normalizing, splitting multiallelic variants an…