User: sonia.olaechea

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Posts by sonia.olaechea

<prev • 22 results • page 2 of 3 • next >
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vcf-merge outputting all genotypes as ./.
... Hi all, I'm trying to merge 2 whole-genome vcf files with different individuals with `vcf-merge`. The program generates seems to merge both files but, surprisingly, it puts a `./.` in all the SNPs of the second file (as if they hadn't been genotyped, but they have!) I've also tried to merge both f ...
vcf vcf-merge written 29 days ago by sonia.olaechea50
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PGDSPider VCF to BAYENV
... Hi all, I'm trying to convert my VCF file to Bayenv2 format with PGDSpider 2.1.1.5. My problem is that it recognises a lot of SNPs as non-polymorphic (although they actually are...). I've realised that some of my SNPs have in the VCF REF column more than just one alelle (I guess they are insertion ...
vcf bayenv2 pgdspider written 4 weeks ago by sonia.olaechea50
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spid file in PGDSpider-cli
... Hi all! I'm trying to convert a VCF file to Bayenv2 format with PGDSpider command line version. However, I cannot find a way to generate the spid file in the terminal version of the program (I wanted to avoid, if possible, downloading the GUI version of the program). Does anyone know how to do it? ...
spid pgdspider written 4 weeks ago by sonia.olaechea50
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Comment: C: Beagle imputation results quality control
... Hi eyb, I know it's been several years ago, but right now I'm facing the same problem that you had in that moment: I've just achieved to impute my data with Beagle, but now I would like to know how to filter out the bad quality SNPs. I suspect that it is related with the DR2 field, but I'm not qui ...
written 5 weeks ago by sonia.olaechea50
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Comment: C: 1000Genomes population allele frequencies for list of SNPs
... Sorry, I don't know what might be happening but my plink2 returns that it doesn't recognise the "--pfile" option... I'm launching the command in a folder with the files all_phase3.pgen.zst, all_phase3.psam, all_phase3.pvar.zst and my list of rsIDs... is it possible that it is not recognising some o ...
written 10 weeks ago by sonia.olaechea50
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1000Genomes population allele frequencies for list of SNPs
... Hi all, I have a list of more than 100 SNPs (rsXXXXXX) and I would like to obtain the different allele frequencies that each of them shows in each of the 1000Genomes populations (if possible not manually...). Is there any tool, R package etc, that allows to download them all at once? I've thought t ...
1000genomes snps written 11 weeks ago by sonia.olaechea50 • updated 11 weeks ago by Pierre Lindenbaum116k
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split vcf by individual
... Hi all! I have a vcf file which contains 2 regions (in different chromosomes) for a group of individuals. I'm trying to split this vcf just by individual. The file IDlist.txt contains the IDs of all the individuals. The command I'm using is the following: for i in $(cat IDlist.txt); do i=" ...
vcf vcf-subset vcftools snp written 12 weeks ago by sonia.olaechea50 • updated 12 weeks ago by Paul1.3k
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Answer: A: vcftools --TajimaD in sliding windows
... Hey again, it looks like vcf-kit is more straightforward for calculating Tajima's D value in sliding windows! To be honest, I haven't been really able to make PopGenome function, but vcf-kit is quite easy: vk tajima 5000 3000 input.vcf > output.TajimaD 5000 refers to the window size and 30 ...
written 3 months ago by sonia.olaechea50
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mean Tajima's D value
... Hi all, I have calculated Tajima's D value for several windows in my data. Some of those windows contain just 1 or 2 SNPs, so I would like to combine their Tajima's D value into one (of a bigger region). Is it enough with calculating the mean Tajima's D value of those smaller regions or is there so ...
tajima's d snp written 3 months ago by sonia.olaechea50 • updated 3 months ago by pltbiotech_tkarthi70
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Comment: C: vcftools --TajimaD in sliding windows
... Thanks a lot, Kevin! I'm working on VCF-kit (I'm having trouble with the installation) and I've also found an R package called PopGenome that calculates several population genomics statistics in sliding windows... Let's see which of both is better ;) ...
written 3 months ago by sonia.olaechea50

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