User: always_learning

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Posts by always_learning

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Comment: C: Best tool for variant calling
... Hi Kevin, Do you suggest the same pipeline across PANEL and exome data as well? Thanks Najeeb ...
written 3 months ago by always_learning970
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Comment: C: Best tool for variant calling
... Regarding this point 4: Produce random BAM subsets per sample (usually 3 subsets at 25%, 50%, and 75% 'randomly' selected reads) Could you please explain the procedure or provide the command used? Thanks Najeeb ...
written 3 months ago by always_learning970
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Comment: C: VCFParseError: ploidy > 2 not supported
... I think "genotype get set to unknown" will be a better approach. What do you think? ...
written 5 months ago by always_learning970
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Comment: C: VCFParseError: ploidy > 2 not supported
... I can't run this again. This is merged VCF of around 6000 samples. I think It will fine to remove such sites from VCF. ...
written 5 months ago by always_learning970
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VCFParseError: ploidy > 2 not supported
... I have few SNP with ploidy > 2 in my VCF(Human) generated by GATK with genotypes like "0/1/1". Any idea how I can remove them from my VCF file? Any tools that do that? ...
vcf gatk ploidy written 5 months ago by always_learning970 • updated 3 months ago by tpoterba50
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Comment: C: AF comparison between two population.
... Thanks !! But I have just frequencies !! So I don't think that I can do similar to that. ...
written 9 months ago by always_learning970
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Comment: C: AF comparison between two population.
... Please find dropbox link for example data. https://www.dropbox.com/s/1gjnoh1ft6k0aat/example.txt?dl=0 ...
written 9 months ago by always_learning970
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Comment: C: AF comparison between two population.
... Please find dropbox link for example file. https://www.dropbox.com/s/1gjnoh1ft6k0aat/example.txt?dl=0 ...
written 9 months ago by always_learning970
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Comment: C: AF comparison between two population.
... What is not clear in my Question? ...
written 9 months ago by always_learning970
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AF comparison between two population.
... Hi, I have Allele Frequenct frequency data for Population A and I wanted to compare this with Population B. Below is the script that I wrote for Chi Square test between AF for these two population. *** library("dplyr") input = fread("GENE_PANEL_MUTATION.tsv", sep = "\t") inputTtest = ...
r statistical test af written 9 months ago by always_learning970

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Good Question 11 months ago, asked a question that was upvoted at least 5 times. For Homozygous Indel/Snp & Heterozygous Indel/Snp
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