User: biogirl

gravatar for biogirl
biogirl190
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190
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European Union
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1 month, 2 weeks ago
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j*************@imperial.ac.uk

Posts by biogirl

<prev • 64 results • page 1 of 7 • next >
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vcftools Tajima's D calculation
... Hi all, I'm running vcftools on a vcf (obv, ha) to calculate Taijma's D in sliding windows of 10,000 bp: vcftools --vcf in.vcf --out tajimasd --TajimaD 10000 The log file states that after filtering, kept 342087 out of a possible 342087 Sites (so all sites). Yet when I look at the output file ...
vcftools tajimasd selection written 8 weeks ago by biogirl190
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Comment: C: Convert haploid to homozygous diploid
... Yeah I have the BAMs, I was considering recalling the SNPs in diploid mode (with gatk). I'm a little confused how --samples-file would help in this situation though, can you expand please? ...
written 9 weeks ago by biogirl190
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Convert haploid to homozygous diploid
... Hi, Hoping someone can sanity check my idea. I’m working on a haploid genome and called SNPs. I want to calculate genome-wise Tajima’s D (I’m sliding windows) using vcftools, but this only works on diploid SNP calls. If I were to re-call my SNPs in diploid mode, then my SNPs should come up as h ...
snp written 9 weeks ago by biogirl190
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Comment: C: Association test in Plink
... Done https://www.biostars.org/p/397884/ ...
written 4 months ago by biogirl190
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bcftools merge creates high missingness rate
... Hi (again), Posting this as a new topic. I've been trying to run an association test in plink, but it seems the rate of missingness in the merge vcf is high, meaning all copies of the second allele have been replaced with missing genotypes. Therefore, all of my variants have a MAF of 0. This is th ...
bcftools plink vcftools written 4 months ago by biogirl190
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Comment: C: Association test in Plink
... Oh wow, ok! Thanks for that. I realise this is bordering on a new topic now (and perhaps I should make a new thread?) but any ideas on how to fix the vcf? I merged all my vcfs into one using bcftools: bcftools merge --force-samples *vcf.gz -o all_isolates.vcf Where all the individuals vcfs had ...
written 4 months ago by biogirl190
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Comment: C: Association test in Plink
... Cool, thanks for that - that has solved the issue of replacing the '0' with the reference allele - so I'm actually getting nucleotides for A1 and A2 now. But I'm still not getting values for CHISQ, P or OR - they are still all NA when I try to test for association: plink --bfile pleasework -- ...
written 4 months ago by biogirl190
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Comment: C: Association test in Plink
... Sure! Here's the `.log` output: Options in effect: --allow-extra-chr --allow-no-sex --assoc --file GWAS Random number seed: 1567672357 193423 MB RAM detected; reserving 96711 MB for main workspace. Scanning .ped file... done. Performing single-pas ...
written 4 months ago by biogirl190 • updated 4 months ago by zx87548.9k
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Comment: C: Association test in Plink
... It doesn't retain the reference - it just puts that as '0' and keeps the SNPs as nucleotides. This is how I've been making my .ped files ...
written 4 months ago by biogirl190
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Comment: C: Association test in Plink
... Ok I think I know what the problem is - when converting from vcf to .ped, the SNPs are kept as nucleotides (A,C,G,T) but the reference is left as '0'. So I have a mixture of 0 and nucleotides in the .ped file. Any idea on how to convert from vcf to bed and retain the reference allele, instead of ge ...
written 4 months ago by biogirl190

Latest awards to biogirl

Student 9 weeks ago, asked a question with at least 3 up-votes. For PSMC using haploid genomes
Popular Question 15 months ago, created a question with more than 1,000 views. For SNPs only output from bcftools
Great Question 2.6 years ago, created a question with more than 5,000 views. For SNPs only output from bcftools
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Analysis past the differentially expressed genes: RNAseq
Popular Question 2.6 years ago, created a question with more than 1,000 views. For PLINK error locus has more than 2 alleles
Popular Question 2.6 years ago, created a question with more than 1,000 views. For SNPs only output from bcftools
Popular Question 2.6 years ago, created a question with more than 1,000 views. For ddRADseq and segregating SNPs
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Arabidopsis GFF files
Popular Question 2.7 years ago, created a question with more than 1,000 views. For PLINK error locus has more than 2 alleles
Student 2.9 years ago, asked a question with at least 3 up-votes. For PSMC using haploid genomes
Popular Question 3.0 years ago, created a question with more than 1,000 views. For PLINK error locus has more than 2 alleles
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Binary SNP matrix into APE (R)
Popular Question 4.2 years ago, created a question with more than 1,000 views. For SNPs only output from bcftools
Popular Question 4.3 years ago, created a question with more than 1,000 views. For SNPs only output from bcftools
Popular Question 4.6 years ago, created a question with more than 1,000 views. For SNPs only output from bcftools
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