User: irieljoerin

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irieljoerin40
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40
Status:
New User
Location:
Brazil/Curitiba/Universidade Federal do Paraná
Last seen:
2 days, 9 hours ago
Joined:
10 months ago
Email:
i**********@gmail.com

Posts by irieljoerin

<prev • 19 results • page 1 of 2 • next >
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Method for estimation of subcontinental admixture from haplogroup data
... Hi all, I would like to know if there exist any bioinformatic tool, R package, or free access software for estimation of subcontinental admixture proportions of populations from haplogroup data. Any advice would be helpful! ...
mtdna admixture haplogroup y chromosome written 4 weeks ago by irieljoerin40
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Filter only SNPs in 1000 Genomes Data Slicer
... Hi all, I´m trying to retrieve genotypic data from 70 SNPs (from different chromosomes) from certain 1000 Genomes populations. I plan to use Data Slicer to create vcf for each variant and then merge them all in R with VariantAnnotation package. However, when I create the vcf in Data Slicer structura ...
data slicer 1000 genomes vcf snp written 5 weeks ago by irieljoerin40 • updated 5 weeks ago by harold.smith.tarheel4.6k
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Comment: C: How to check mitochondrial reference in GWAS data for HaploGrep analysis
... I have switched the complementary strands and corrected the ancestral and alternative alleles of my vcf file to agree with rCRS. I think the problem was that my files were created with plink, which assigns ancestral and alternate alleles according to their frequency in the sample, and not to the rea ...
written 7 weeks ago by irieljoerin40
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Comment: C: How to check mitochondrial reference in GWAS data for HaploGrep analysis
... Thanks a lot for your help, Jeremy! I will try to create the hsd file and check my results. ...
written 8 weeks ago by irieljoerin40
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Comment: C: How to check mitochondrial reference in GWAS data for HaploGrep analysis
... Yes, the chip was Infinium CoreExome-24 v1.1 ...
written 8 weeks ago by irieljoerin40
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Comment: C: How to check mitochondrial reference in GWAS data for HaploGrep analysis
... Yes, 1/1 means a difference from reference as I understand. This file was converted with plink from a plink (.ped) file obtained from microarray, so some variants are genotyped according to different strands of the reference. But I run HaploGrep with the chip flag. Do you think it does not consider ...
written 8 weeks ago by irieljoerin40
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Comment: C: How to check mitochondrial reference in GWAS data for HaploGrep analysis
... I had to eliminate a few positions due to the character limit, and the columns ID, INFO (PR) and FORMAT (GT). The chip variant IDs are: ID 2010-08-MT-841 2010-08-MT-981 200610-102 2010-08-MT-550 exm-rs41531144 MitoT217C exm-rs41323649 MitoG228A 200610-105 exm2263307 exm-rs41528348 MitoC295T exm22161 ...
written 8 weeks ago by irieljoerin40
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Comment: C: How to check mitochondrial reference in GWAS data for HaploGrep analysis
... POS REF ALT 5 72 A G 0/0 93 A G 0/0 125 A . 0/0 215 A G 0/0 217 A . 0/0 217 A . 0/0 228 G A 0/0 228 G A 0/0 236 A G 0/0 285 G . 0/0 295 G A 0/0 295 G A 0/0 418 G A 0/0 456 G A 1/1 477 A G ./. 489 A G ./. 499 G A ./. 606 A . 0/0 629 A . 0/0 710 A G 0/0 711 A . 0/0 722 G . 0/0 750 G A 0/0 921 A G 0/0 ...
written 8 weeks ago by irieljoerin40
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Comment: C: How to check mitochondrial reference in GWAS data for HaploGrep analysis
... How can I show you one of my genotypes? It seems that I cannot post more than 5000 characters. ...
written 8 weeks ago by irieljoerin40
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Comment: C: How to check mitochondrial reference in GWAS data for HaploGrep analysis
... Thanks, Jeremy for your answer! Yes, my data is from microarray. I have already checked manually some positions in my plink file to see if the genotypes agree with those found in rCRS/NC_012920.1, and all them agree. Also, I recently saw in the chip manifest that several variants were obtained fro ...
written 8 weeks ago by irieljoerin40

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