User: always_learning
always_learning • 970
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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_learning • 970
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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_learning • 970
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... I think "genotype get set to unknown" will be a better approach. What do you think? ...
written 5 months ago by
always_learning • 970
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... 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_learning • 970
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... 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? ...
written 5 months ago by
always_learning • 970
• updated
3 months ago by
tpoterba • 50
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... Thanks !! But I have just frequencies !! So I don't think that I can do similar to that. ...
written 9 months ago by
always_learning • 970
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... Please find dropbox link for example data.
https://www.dropbox.com/s/1gjnoh1ft6k0aat/example.txt?dl=0 ...
written 9 months ago by
always_learning • 970
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... Please find dropbox link for example file.
https://www.dropbox.com/s/1gjnoh1ft6k0aat/example.txt?dl=0 ...
written 9 months ago by
always_learning • 970
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... What is not clear in my Question? ...
written 9 months ago by
always_learning • 970
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... 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 = ...
written 9 months ago by
always_learning • 970
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