User: dec986

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dec986230
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Posts by dec986

<prev • 138 results • page 1 of 14 • next >
4
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how to add reference alleles to VCF?
... I’m converting gVCFs to VCF, but the reference alleles are missing. An example below: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 180525_FD02929177 1 97547947 . T . . . DP=31 GT:DP:RGQ 0/0:31:81 1 97915614 . C . . . DP=40 GT:DP:RGQ 0/0:40:99 1 97981343 . A . . . DP=43 GT:DP:RGQ 0 ...
vcf genome written 4 weeks ago by dec986230 • updated 4 weeks ago by RamRS30k
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how to split M3VCF by ID?
... I'm attempting to extract sample IDs from an m3vcf file just like I would with VCF, with a command like: bcftools view --samples XXXXX Estimates.m3vcf.gz but then I get an error: `Failed to open Estimates.m3vcf.gz: unknown file type` My instinct is that bcftools doesn't support the m3vcf ty ...
imputation written 5 weeks ago by dec986230
3
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Plink altering VCF IDs
... I'm running a VCF command thus: plink --vcf chrX.M.vcf.gz --set-hh-missing --output-chr M --recode vcf --out chrX.M.set_hh_missing but the output is distorted in that the sample IDs are doubled, for example `ABCDEF` becomes `ABCDEF_ABCDEF` None of the options seem like they would do this, af ...
plink written 7 weeks ago by dec986230 • updated 7 weeks ago by chrchang5237.3k
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conversion of VCF to M3VCF using Minimac
... I'm attempting to convert a VCF into a M3VCF. I've been looking at https://genome.sph.umich.edu/wiki/M3VCF_Files and https://genome.sph.umich.edu/wiki/Minimac3 and supposedly minimac3 can convert, but the exact command line syntax is a mystery. I've tried `Minimac3 --refHaps chrX.F.vcf.gz --proces ...
minimac written 8 weeks ago by dec986230 • updated 4 days ago by awakumaya0
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Comment: C: How to extract sample IDs from VCF into new VCF?
... Indeed, this is the solution ...
written 3 months ago by dec986230
2
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1
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How to extract sample IDs from VCF into new VCF?
... 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 ...
vcf written 3 months ago by dec986230
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Comment: C: Can Plink 1.07 set-hh-missing output VCF?
... `~/Scripts/plink1.9/plink --vcf ZZQDBCZE.chrX.vcf.gz --set-hh-missing --out tmp --recode vcf` is the correct answer to my question ...
written 3 months ago by dec986230
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Comment: C: Can Plink 1.07 set-hh-missing output VCF?
... I kept seeing beta for Plink 1.9, which made me think that it's not ready ...
written 3 months ago by dec986230
4
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Can Plink 1.07 set-hh-missing output VCF?
... 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. ...
plink written 3 months ago by dec986230 • updated 3 months ago by chrchang5237.3k
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Comment: C: Cannot find faToTwoBit download
... thank you!! danke schön!! ...
written 3 months ago by dec986230

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