User: mab658

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mab65880
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Posts by mab658

<prev • 19 results • page 1 of 2 • next >
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how to estimate founder and effective population size from snps data in VCF format
... Hi everyone, I have a filtered SNPS sequence data in VCF format. I need to use this data to estimate the founder size and effective population size (Ne). I have no idea of how to go about it. I got to know the Ne could be estimated through linkage disequilibrium and heterozygote excess. Could anyon ...
snp written 10 months ago by mab65880 • updated 10 months ago by GenoMax95k
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how to obtain imputation accuracy - allelic R2 in beagle
... Dear All, I used beagle for imputation but I could not see the allelic Rsquare (AR2) which measures the imputation accuracy in my new imputed vcf file named imputed_file. Is there anything missing in my script? I got to know that "ref=' argument which refers to reference data is required to get impu ...
snp beagle written 20 months ago by mab65880 • updated 20 months ago by zx87549.9k
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Obtain VCF format file from imputed dosage format file using beagle2vcf
... Please how do I use this expression to convert imputed snps data in dosage format to VCF format java -jar beagle2vcf.jar [chrom] [markers] [bgl] [missing] > [vcf] An example will give me a better understanding. I don't understand what the option [markers], [bgl], and [missing] actually stan ...
snp written 20 months ago by mab65880 • updated 15 months ago by kas0
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Comment: C: How to combine chromosome vcf files
... Hi Pierre, I wanted to merge VCF files which had already splitted by chromosones into a single file. Though each is compressed i.e. chr1.vcf.gz, chr2.vcf.gz, ......chrn.vcf.gz. I could not see any an output file merged.vcf.gz when I used the command. Is it because the file is compressed? java ...
written 24 months ago by mab65880
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Comment: C: Calculate mean_GQ value from individual GQ values in a multi-sample VCF file
... This is what I have been looking for. I applied it to my work and it went well. I have chrom, pos, and sample with their respective GQ values. How do I get the average across all the samples for each site (i.e chrom and pos). I need the average so that I can plot it in R. ...
written 2.0 years ago by mab65880
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how to generate genetic maps from VCF snps data
... Hi Everyone, Could someone guide me on how to generate genetic map from snps VCF file in order to use it for imputation. I have filtered my snps VCF file and I need genetic map for the imputation. I got to know that one can use PLINK. I need to know what I need to extract from my data prior to us ...
snp sequencing written 2.1 years ago by mab65880 • updated 8 months ago by Kevin Blighe69k
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why filtering sites with allele count below 3
... Hi everyone, I came across SNP filtering tutorial where the author used the flag `--mac 3` to filter SNPs that have a minor allele count less than 3. That is `vcftools --vcf input_file.vcf --mac 3 --recode --out filtered_file` Could someone explain to me why filtering out sites with minor allele ...
snp sequencing written 2.1 years ago by mab65880 • updated 2.1 years ago by Jean-Karim Heriche24k
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Comment: C: How to filter vcf file on minimum genotype depth and quality for each sample
... from the above script, --minGQ and --minDP take the value of 15 and 10 respectively for filtering genotype quality and depth. Is there any criteria for choosing 15 and 10.. Just to know if 15 and 10 are standard values to use for those flags. ...
written 2.1 years ago by mab65880
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Conversion of imputed VCF file to HapMap format
... Hi Everyone, I have successfully imputed my VCF file using beagle4.1. How do I convert it to HapMap format, please? Thanks. ...
rna-seq snp written 2.1 years ago by mab65880 • updated 2.1 years ago by 159932162500
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Comment: C: Filtering of low coverage variants from VCF
... Dear All, I am having similar problem in determining the appropriate filtering criteria for the snps depth and quality. I am just a beginner in using `vcftools` for snps call filtering.How do i translate the hard filters below using vcftools: that is QualByDepth (QD) 2.0 FisherStrand (FS) 60.0 RMSMa ...
written 2.1 years ago by mab65880

Latest awards to mab658

Popular Question 20 months ago, created a question with more than 1,000 views. For Conversion of imputed VCF file to HapMap format
Popular Question 20 months ago, created a question with more than 1,000 views. For Imputation of vcf file
Popular Question 20 months ago, created a question with more than 1,000 views. For filter out subset of samples from vcf file

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