User: emyli
emyli • 0
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Posts by emyli
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... Hi there,
I have whole genome sequencing data I am using to look for novel variants. I have filtered the data and have a short list of potential novel variants - so now I want to validate if they are truly present in my DNA sample or some sort of sequencing artefact, by PCR amplification. However, ...
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... Thanks for your comments. This actually isn't a line I want to include, I just used it as an example of what the INFO column looks like. The command doesn't actually work at all, and outputs an error saying INFO/Gene.refGene is not in the VCF header, and I am trying to understand why that is. ...
written 16 months ago by
emyli • 0
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... Hi,
I have a VCF that has been annotated using ANNOVAR. I am trying to subset the VCF based on the value contained in the INFO column field of "Gene.refGene=". I am trying to use bcftools for this (see below), however there is no mention of this field, or any fields added by ANNOVAR, in the VCF hea ...
written 16 months ago by
emyli • 0
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... Hi there,
I generated a VCF using plink from .ped and .map files from a genotyping experiment as so:
plink --file test --recode vcf --out testVCF
As is well documented, this assigned the REF alleles in the output VCF to be the major allele observed in the data.
I am trying to recode to make ...
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Comment:
C: PLINK2 recode ped flag issue
... Thanks for the suggestion, I believe this is the version I have been using (binary download ofStable (beta 4.6, 15 Aug) for OS X (64-bit) from https://www.cog-genomics.org/plink2). I tried again using your modified command and am getting the same result, I am using checkVCF.py to assess the validity ...
written 16 months ago by
emyli • 0
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... Hi,
I am trying to covert .ped and .map files to a VCF file using plink2, as in the examples below:
plink2 --ped test.ped --map .test.map --recode vcf --out testVCF
plink2 --file test --recode vcf --out testVCF
However, I am thrown the errors:
Error: Unrecognized flag ('--ped').
...
written 16 months ago by
emyli • 0
• updated
16 months ago by
tarek.mohamed • 240
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... Works perfectly, thank you! ...
written 16 months ago by
emyli • 0
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... I have a .ped file generated using SNP chip .idat data processed using the GenomeStudio GT module. The genotypes are coded using allele values of 1, 2 , 3 or 4. Is there a away to convert these to the base call ie. A, C, G or T? I assume each number corresponds to a base call, but am unsure of how t ...
written 16 months ago by
emyli • 0
• updated
16 months ago by
tarek.mohamed • 240
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Comment:
C: What does ALT 0 mean in a VCF?
... Firstline says ##fileformat=VCFv4.2 ...
written 17 months ago by
emyli • 0
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Comment:
C: What does ALT 0 mean in a VCF?
... Thanks, that is useful. This is actually generated from the ANNOVAR output .txt file (which I understand to be a more visually friendly version of the corressponding VCF). ...
written 17 months ago by
emyli • 0
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