User: sonia.olaechea

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Posts by sonia.olaechea

<prev • 34 results • page 2 of 4 • next >
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LD filter for GWAS with plink
... Hi all, I'm trying to remove SNPs that are in linkage disequilibrium (r2 = 0.8) from my GWAS dataset. For the moment, I've been trying the following command: `plink --vcf myvcf.vcf --const-fid 0 --r2 --ld-window-r2 0.8 --recode vcf --out myvcf.out` It actually works and generates a `.ld`output fi ...
gwas linkage disequilibrium plink written 5 months ago by sonia.olaechea90
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Comment: C: Beagle imputation results quality control
... Great, thanks, I'll have that in mind! ...
written 5 months ago by sonia.olaechea90
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Comment: C: update genotypes in vcf
... Okey, I'll try that, thanks! ...
written 6 months ago by sonia.olaechea90
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Comment: C: update genotypes in vcf
... Okey, right, thanks :)! But then, how do I change the genotypes? Still with my `sed` command?? Or somehow with Python? ...
written 6 months ago by sonia.olaechea90
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update genotypes in vcf
... Hi all, Recently, I've had some trouble with a VCF file in which a program had turn around my REF and ALT fields (e.g. REF=C, ALT=T, but should be REF=T, ALT=C) and also their related genotypes. I've managed to turn around the REF and ALT fields, but I'm not able to update my genotypes in an effi ...
vcf genotypes written 6 months ago by sonia.olaechea90
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Comment: C: Change ALT field in VCF
... head ALT.txt rs10032042 G rs10174691 C rs10221923 G rs10223644 G rs1028771 C rs10305678 G rs10404081 G rs10421281 C rs1042478 G rs10459252 C` file ALT.txt file ALT.txt: ASCII text` ...
written 6 months ago by sonia.olaechea90
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Change ALT field in VCF
... Hi all, I have 2 vcf files for the same positions but with different individuals which I would like to merge. However, in one of the files some of my variants have a `.` in the ALT field, which I would like to replace by the corresponding allele. I've tried to obtain those alternatives alleles from ...
vcf gwas snps written 6 months ago by sonia.olaechea90
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Comment: C: vcf-merge outputting all genotypes as ./.
... Hi @finswimmer! Yes, you were right, it hasn't worked :( So, right now I'm trying to fix the REF alleles using `bcftools` plugin `+fixref`. I've launched this command: bcftools +fixref myfile1.vcf.gz -- -f hg37.all.fa.gz And it returns this output: # SC, guessed strand convention SC ...
written 7 months ago by sonia.olaechea90
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Comment: C: vcf-merge outputting all genotypes as ./.
... Hi again! It turns out data `myfile1.vcf` comes from a chip and `myfile2.vcf` from a sequencing process (and it has been aligned afterwards)!! Both vcfs have as a reference hg19, but `myfile2.vcf' has more SNPs than the other file! So I guess I will generate a list of the SNPs in `myfile1.vcf`, ext ...
written 7 months ago by sonia.olaechea90
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Comment: C: vcf-merge outputting all genotypes as ./.
... Oh, yes, we have a problem! The only thing I can find in the header that could give us a clue is `##source:PLINKv1.90` and `##INFO=` , what is actually not very informative, right' By the way, I've tried changing the chromosomes names in the first column and it still gives an error, so I guess the ...
written 7 months ago by sonia.olaechea90

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