User: seta

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seta1.2k
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Posts by seta

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GCTA tool for case-control association analysis
... Dear all, I found here, GCTA is a suitable tool for doing association analysis of both related and unrelated samples as it account for sample relatedness yes? But the MLM (mixed linear model) option within GCTA is just for quantitative traits, could you please let me know if there is any option to ...
case-control gcta written 6 weeks ago by seta1.2k • updated 6 weeks ago by Lemire560
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Comment: C: use `plink --rel-cutoff` to remove related samples
... Hi chrchang523, Although it's late, I read the corresponding paper; but the question is still remaining. Could you please let me know which value should be selected for `--rel-cutoff` for removing related individuals with 2th degree of relationship? Thanks ...
written 6 weeks ago by seta1.2k
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Comment: C: Variant association analysis with both related and unrelated individuals
... Thank you very much. ...
written 6 weeks ago by seta1.2k
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Variant association analysis with both related and unrelated individuals
... Dear all, I'm going to do an association analysis of a set of common SNPs with some binary and quantitative traits, encompassing both related and unrelated individuals. As far as I know the package such as plink considered just unrelated samples, so it isn't appropriate for my case. Could you pleas ...
package/tool association analysis releatedness written 7 weeks ago by seta1.2k • updated 7 weeks ago by Lemire560
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Comment: C: How to get rsid during the variant annotation using VEP (offline mode)
... it's my mistake; actually, I thought the "check_existing" is considered by VEP as default. Now, with adding this item, the issue was solved. ...
written 12 weeks ago by seta1.2k
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Comment: C: How to get rsid during the variant annotation using VEP (offline mode)
... Thanks Emily; I annotated VCF file of chromosome 22 and the "Existing_variation" column of output is empty, so what's happened in your view? ...
written 12 weeks ago by seta1.2k
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How to get rsid during the variant annotation using VEP (offline mode)
... Dear all, I've got a large list of variant as VCF format per chromosome (human), which annotated using VEP (release 98) as offline mode. But, I didn't get the corresponding rsid at the output. Could you please help me out how I can obtain the "rsid" during the annotation? Thanks ...
ensembl vep annotation written 12 weeks ago by seta1.2k • updated 12 weeks ago by Emily_Ensembl20k
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Comment: C: How to get sample names and genotype for SNP in multi-sample VCF file
... Hi Kevin, I used your code with some modification to add AC,AN, and AF as I change `(bcftools query -f '[\t%SAMPLE=%GT]\n` `MyVariants.Norm.vcf to bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%AC\t%AN\t%AF[\t%SAMPLE=%GT]\n' MyVariants.Norm.vcf` | and also removing the first part paste <(bc ...
written 3 months ago by seta1.2k
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Gene distance for assigning the intergenic variants
... Dear all, I have got a list of annotated variants derived from human whole genome sequencing, which the intergenic variants were assigned to several genes along with the corresponding gene distance. I was wondering how it can be reliable? and could you please let me know the acceptable gene distanc ...
annotation intergenic snp gene distance written 3 months ago by seta1.2k
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Comment: C: The VEP output for the variants of whole genome sequencing
... Thanks Emily, I edited the post. The multi-allelic variants already spilt, so I should use the pick per variant. ...
written 3 months ago by seta1.2k

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