User: BAGeno

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BAGeno20
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Posts by BAGeno

<prev • 26 results • page 1 of 3 • next >
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Comment: C: VEP and Annovar Annotation
... I want two things First is annotation of whole genome. Second is to check pharmacogenomically important deleterious variants in whole genome so what do you think which one is most suitable for these tasks. ...
written 12 weeks ago by BAGeno20
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Comment: C: VEP and Annovar Annotation
... I am using these options --sift b, --polyphen b, --ccds, --hgvs, --symbol, --regulatory, --biotype ...
written 12 weeks ago by BAGeno20
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Comment: C: VEP and Annovar Annotation
... I am using standalone VEP ...
written 12 weeks ago by BAGeno20
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VEP and Annovar Annotation
... Hi, I am trying to figure out which tool VEP or Annovar, is most accurate in terms of SIFT and Polyphen annotation. I annotated my file with both Annovar and VEP. I got about 2386 SIFT deleterious variants and 1547 Polyphen deletrious from annovar. And from VEP I got 37323 SIFT deleterious and 26 ...
annovar vep written 3 months ago by BAGeno20
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Comment: C: Downloadable Pharmacogenomic Databases
... Can you post a link? I searched but did not find it ...
written 3 months ago by BAGeno20
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Comment: C: Vcftools gives error when extracting snps
... I tried it and it worked. Thanks ...
written 3 months ago by BAGeno20
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Comment: C: Vcftools gives error when extracting snps
... I took command from here. https://www.biostars.org/p/61371/ ...
written 3 months ago by BAGeno20
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Comment: C: Vcftools gives error when extracting snps
... vcftools --vcf --snps --recode --recode-INFO-all This is the command I typed on terminal. ...
written 3 months ago by BAGeno20
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Vcftools gives error when extracting snps
... Hi, I want to extract SNPs from vcf based on list of rsids. From this I used command `vcftools --vcf --snps --recode --recode-INFO-all` But it is giving me error. stat error: No such file or directory Error: Can't determine file type of --recode-INFO-all Please tell me how to correct i ...
vcftools snp written 3 months ago by BAGeno20
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Comparing rsids in two VCF
... Hi I have two VCF and I want to find common rsids in those two files. For this purpose I have used grep command by taking list of rsids from one file and running it on other file, but it gave me some extra rsids as well which were not present in the list. I have also used bcftools isec command but ...
vcf rsid written 4 months ago by BAGeno20 • updated 4 months ago by Pierre Lindenbaum99k

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