User: mostafarafiepour

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Posts by mostafarafiepour

<prev • 161 results • page 1 of 17 • next >
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calculate fst for every allele in any position
... 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 ...
fst snp written 7 weeks ago by mostafarafiepour60
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Separating a region of the VCF file
... 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 ...
vcftools snp written 6 months ago by mostafarafiepour60
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Comment: C: Calculate Fis (inbreeding coefficient)
... 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 6 months ago by mostafarafiepour60
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Calculate Fis (inbreeding coefficient)
... 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 ...
vcftools snp written 6 months ago by mostafarafiepour60 • updated 9 weeks ago by ginushika0
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Calculate heterozygosity for each SNPs in the bim file.
... 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 ...
snp-chip snp written 12 months ago by mostafarafiepour60
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Comment: C: Create a 3-D PCA
... Many thanks dear cpad0112 for your good advice. ...
written 12 months ago by mostafarafiepour60
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Create a 3-D PCA
... 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 ...
R written 12 months ago by mostafarafiepour60
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Calculating Heterozygosity for each SNPs.
... 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) ...
snp written 13 months ago by mostafarafiepour60 • updated 13 months ago by Kevin Blighe53k
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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 13 months ago by mostafarafiepour60
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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 13 months ago by mostafarafiepour60

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Popular Question 6 weeks ago, created a question with more than 1,000 views. For VEP- What is the best idea to start analyzing?
Popular Question 6 weeks ago, created a question with more than 1,000 views. For How Can I Count Snps In My Final Vcf Files
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Size difference between Bam file and sort-bam file
Epic Question 6 months ago, created a question with more than 10,000 views. For Replacing a values from a column in another column
Popular Question 6 months ago, created a question with more than 1,000 views. For Size difference between Bam file and sort-bam file
Popular Question 6 months ago, created a question with more than 1,000 views. For VEP- What is the best idea to start analyzing?
Popular Question 6 months ago, created a question with more than 1,000 views. For Count number of SNPs per chromosome in vcf file
Popular Question 6 months ago, created a question with more than 1,000 views. For How Can I Count Snps In My Final Vcf Files
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Popular Question 12 months ago, created a question with more than 1,000 views. For Size difference between Bam file and sort-bam file
Popular Question 12 months ago, created a question with more than 1,000 views. For Count number of SNPs per chromosome in vcf file
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