User: mostafarafiepour
mostafarafiepour • 70
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Posts by mostafarafiepour
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... Hi Dear all,
I have a table of SNPs with alleles in any position (alleles A1 and A2) (As you can see in the table below).
So, I want to calculate the Fst for each position. I can only calculate Fct for the VCF file but I have no idea about it.
What is the best idea?
SNP Chr Posi ...
written 8 months ago by
mostafarafiepour • 70
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... Hi Dear All,
I'm trying to separate 5Mb to 10Mb region of my VCF file with vcftools. But when I get the output, it only contains a header??
What is the best idea?
Codes I run:
vcftools --vcf My_Chr20.vcf --chr 20 --from-bp 5000000 --to-bp 10000000 --recode --out My_Output
or
...
written 12 months ago by
mostafarafiepour • 70
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... Hi Ram, Many thanks for your reply,
please see here (https://www.biostars.org/p/266502/) for your first question.
I mean by "Fis for population": You said that (plink also has a way to compute inbreeding coefficients, but again, they are done at the individual level), Right? So, my question is, ca ...
written 13 months ago by
mostafarafiepour • 70
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... Hi Dear,
I want to calculate Fis (inbreeding coefficient) for each population (I have a VCF file for each population and my data is whol genome sequencing). After my online search, I came to the conclusion that I have to use the following code to calculate Fis:
vcftools --vcf my_vcf --het --ou ...
written 13 months ago by
mostafarafiepour • 70
• updated
8 months ago by
ginushika • 0
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... Hi all dear,
I have downloaded a database that is related to SNP-chip data. This database contains three files:
![enter image description here][1]
So, i want to Calculate heterozygosity for each SNPs. I use plink --make-bed --file Colli_buffalo_diversity --freqx --out Coli_freqx script to calcul ...
written 19 months ago by
mostafarafiepour • 70
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Comment:
C: Create a 3-D PCA
... Many thanks dear cpad0112 for your good advice. ...
written 19 months ago by
mostafarafiepour • 70
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... Hi all dear,
I have a PCA output:
Pop PC1 PC2 PC3 Population
EAZ01 0.0394502269547468 0.0483472562251034 -0.0803608526481478 EAZ
EAZ02 0.0504868156065647 0.0580742278257349 -0.107896355901351 EAZ
EAZ03 0.03740738709061 ...
written 19 months ago by
mostafarafiepour • 70
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... Hi all dear,
I want to calculating heterozygosity for each SNPs. After studying the plink guide, I have calculated the heterozygosity using the following script.
plink --make-bed --file purebred411_qc --freqx --out freqx_411
And I got this output:
CHR SNP A1 A2 C(HOM A1) C(HET) ...
written 19 months ago by
mostafarafiepour • 70
• updated
19 months ago by
Kevin Blighe ♦ 63k
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Comment:
C: Common SNPs among all populations
... This code works well but with a small change.
$ bcftools view -i 'GT[0-9]="alt" && GT[10-19]="alt" && GT[20-29]="alt" && GT[30-39]="alt" && GT[40-49]="alt"' Final.vcf|grep -v "^#"|wc -l ...
written 20 months ago by
mostafarafiepour • 70
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957
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2
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Comment:
C: Common SNPs among all populations
... I installed the suggested version, but when I run the script, it does not give me the output. And it only displays the content of my VCF file in a graphical and fast way. My expectation is that when i run the script, i will give the number of common PSNs between 5 populations.
i code run:
bcft ...
written 20 months ago by
mostafarafiepour • 70
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