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Hi,
I noticed that the pipeline detects some somatic mutations with VAF = 1 in a specific cell type. Such mutations may be an example of cell-type-specific clonal expansion which may not be true so…
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Hi, professor Ge.
I would like to express my sincere gratitude for the incredible analysis method you have developed. The functionality it offers is truly powerful, and I have greatly appreciated its…
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From https://opain.github.io/GenoPred/pipeline_technical.html#Workflow my understanding is that sumstat_prep step is done independnetly from format_target step, thus internal score files (produced by …
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Joseline said that if the reference file has a lot of Ns, it might throw a lot of SNPs.
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Hello Jiabo Wang, I want to know how I get PVE result For each SNP, because the output of PVE file is only for P values
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Dear developers,
I wonder if it is possible to export SNPs for loci or regions based on annotations derived from the original VCF.
For example, exporting all SNPs with missense variants for gene…
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Hi,
I'm running the following code from Rstudio:
ld_folder="~/data/dms-gwas/opt/gctb_refs/LD_Reference/ukbEUR_Imputed"
for (pheno in c("test")) {
ma_file=paste0("~/data/dms-gwas/sumstats/B…
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Hi Armando and all,
The provided example.ped and .map worked beautifully. However with my own data set, I am constantly facing the error 'Too few bins' despite altering to even NGEN=200, NBIN=200.…
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Hello, sorry to bother you. Currently, I’m using the command `bcftools view -m 2 -M 2 --threads 4 -Ob -o referencePanel.22.bcf referencePanel.vcf.gz` to process my data. My file `referencePanel.vcf.gz…
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Hi, I am trying to run the phasing workflow with the bams files generated previously with the mapping workflow. However I am not getting the fasta files in the results, I just got the bam files (see …