User: dec986
dec986 • 230
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Posts by dec986
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... Indeed, this is the solution ...
written 1 day ago by
dec986 • 230
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... I've written a script that extracts VCF IDs from a large VCF, in order to get a subset of the sample IDs (people).
This script copies the header from the original VCF and simply pastes it into the new one.
I then extract only the sample IDs that I need for each line in the original VCF.
However, I ...
written 1 day ago by
dec986 • 230
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... `~/Scripts/plink1.9/plink --vcf ZZQDBCZE.chrX.vcf.gz --set-hh-missing --out tmp --recode vcf` is the correct answer to my question ...
written 6 days ago by
dec986 • 230
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... I kept seeing beta for Plink 1.9, which made me think that it's not ready ...
written 6 days ago by
dec986 • 230
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... Hello,
I'm running the command
plink-1.07-x86_64/plink --file ZZQDBCZE.chrX.vcf.gz --make-bed --set-hh-missing --out tmp --noweb
but this is outputting a bed file, which I can't use, as I need a VCF.
I either need a way to convert this to tmp.bed to VCF, or a way for plink to output tmp.vcf. ...
written 6 days ago by
dec986 • 230
• updated
6 days ago by
chrchang523 ♦ 7.1k
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Comment:
C: Cannot find faToTwoBit download
... thank you!! danke schön!! ...
written 7 days ago by
dec986 • 230
4
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... I'm looking through the website http://hgdownload.soe.ucsc.edu
and I cannot find the download for the Linux x86_64 faToTwoBit
I downloaded twoBitToFa about a year and a half ago, but cannot find the reverse binary anywhere on the internet now.
I see https://genome.ucsc.edu/goldenPath/help/twoBit ...
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... Hello,
I'm using survminer to try to create a survival formula for a phenotype data set.
library("survival", "survminer")
data <- read.csv(file = "Study.cleaned.csv", header = TRUE)
basic.cox <- coxph(formula = Surv(Observation_time, Event_Detected) ~ Patient_Age + Sex+BMI, data ...
written 6 weeks ago by
dec986 • 230
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... unfortunately, this still keep things in gVCF format :( ...
written 5 months ago by
dec986 • 230
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... the chromosomes all match ...
written 5 months ago by
dec986 • 230
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