hyunminkang
commented
2 years ago Using VCFs from bulk RNA-seq data is not recommended, and it requires a very careful filtering process.
The reason could be (1) ambient RNAs (2) problems in identifying informative sites in VCF (usually common coding SNPs), (3) problems in the genotype processing, (4) lack of informative reads.
Hyun.
On Thu, Jan 13, 2022 at 7:21 AM bpuzek @.***> wrote:
We are trying to run demuxlet with 8 individuals, using the suggested --alpha 0 --alpha 0.5 parameters
We are getting 82% ambiguous calls, 13% doublets and 5% singlets.
As discussed in one of the issues https://github.com/statgen/demuxlet/issues/29 in demuxlet, this can be due to insufficient number of SNP-overlapping reads "due to various reasons". We obtained our .vcf files from bulk RNA-seq data. Would you expect this to be a problem or would you try and change alpha or another parameter?
Many thanks in advance
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We are trying to run demuxlet with 8 individuals, using the suggested
--alpha 0 --alpha 0.5parametersWe are getting 82% ambiguous calls, 13% doublets and 5% singlets.
As discussed in one of the issues in demuxlet, this can be due to insufficient number of SNP-overlapping reads "due to various reasons". We obtained our .vcf files from bulk RNA-seq data. Would you expect this to be a problem or would you try and change
alphaor another parameter?Many thanks in advance