User: jaafari.omid

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jaafari.omid50
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Posts by jaafari.omid

<prev • 51 results • page 1 of 6 • next >
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Comment: C: How should we merge the Chromosome and position columns of a vcf and or .map fil
... Thank you very much for your direction. I wanted to give it a try but apprently it needs vcf files indexed by tabix already. So first I should give index to my vcf file and then use bcftools annotate. Thank you very much for your great help. Regards, Omid ...
written 8 weeks ago by jaafari.omid50
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How should we merge the Chromosome and position columns of a vcf and or .map file to have the ID column without dots?
... Hi dears all, I have a .map file (from plink) and of course before that a .vcf file which the ID column is just dot. So when I want to do GWAS using GenABEL package I get face with an error and apparently it is because of the marker ID column that all of them are dots. So I must have actually speci ...
vcf plink snp written 8 weeks ago by jaafari.omid50 • updated 8 weeks ago by WouterDeCoster40k
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Comment: C: rename samples in a vcf or plink file
... Thank you very much. It worked properly. Regards, Omid ...
written 8 weeks ago by jaafari.omid50
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Comment: C: rename samples in a vcf or plink file
... Thank you for your answer. I will give it a try and hope it work. Cheers, Omid ...
written 9 weeks ago by jaafari.omid50
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Comment: C: rename samples in a vcf or plink file
... Thank you so much, I will check it. regards, Omid ...
written 9 weeks ago by jaafari.omid50
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rename samples in a vcf or plink file
... Hello dears all, Actually I have a vcf file which it has been generated through samtools/bcftools pipeline. This file doesn't have just the sample names, indeed it has the samples' PATH in it. So what I want to do is removing the PATH and simply just keep the sample names. Moreover, if it is possib ...
vcf plink snp written 9 weeks ago by jaafari.omid50 • updated 9 weeks ago by WouterDeCoster40k
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Error in GWAS using GenABEL package
... Hello dears all, Actually I am running a plink data set (of a fish species) for GWAS using GenABEL package in R. The plink files have been generated from an imputed vcf file. Here is the command that I used for imputation using Beagle: java -Xms1000g -Xmx1000g -jar beagle.28Sep18.793.jar gt=sn ...
genome R next-gen snp gwas written 11 weeks ago by jaafari.omid50
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Comment: C: Depth of coverage
... Thank you very much for your kind and helpful answers. ...
written 5 months ago by jaafari.omid50
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Comment: C: Depth of coverage
... Thank you very much for your giving great help and sight view. As last question can you please tell me why I should use > BCFtools not *vcftools*? ...
written 5 months ago by jaafari.omid50
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Comment: C: Depth of coverage
... Hello dear Kevin, Yes I have read all it already but still I have some misunderstanding. Actually the DP in bcftools filter is solved but the --minDP option in vcftools is different from the depth out put which we take from samtools per each sample? Let's say I have a sorted.bm file and I use the fo ...
written 5 months ago by jaafari.omid50

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