User: dec986
dec986 • 230
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Posts by dec986
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4
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... 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 ...
0
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... 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 ...
written 5 weeks ago by
dec986 • 230
3
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1
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... 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 ...
written 7 weeks ago by
dec986 • 230
• updated
7 weeks ago by
chrchang523 ♦ 7.3k
0
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1
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152
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... 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 ...
0
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193
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... Indeed, this is the solution ...
written 3 months ago by
dec986 • 230
2
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1
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193
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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 3 months ago by
dec986 • 230
0
votes
1
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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 3 months ago by
dec986 • 230
0
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1
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133
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1
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... I kept seeing beta for Plink 1.9, which made me think that it's not ready ...
written 3 months ago by
dec986 • 230
4
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1
answer
133
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1
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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 3 months ago by
dec986 • 230
• updated
3 months ago by
chrchang523 ♦ 7.3k
1
vote
1
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229
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1
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Comment:
C: Cannot find faToTwoBit download
... thank you!! danke schön!! ...
written 3 months ago by
dec986 • 230
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