User: curious

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curious450
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Posts by curious

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Answer: A: CSV file pandas error
... Usually this means there is a header you are not skipping correctly. ...
written 7 days ago by curious450
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Comment: C: How to do a Haplotype based GWAS?
... Hi Kevin, I am in a similar position. I am interested in testing the association between some predetermined haplotypes and phenotype. I have dosage data from an imputation, looks something like this: ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= #CHROM POS ID REF ALT ...
written 11 days ago by curious450
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Is it pretty common to have "reverse complemented alleles" when lifting over a vcf from hg19 to hg38?
... I just lifted over a VCF from hg19 to hg38 using `LiftoverVcf` from GATK. I noticed a lot of the alleles have the field `ReverseComplementedAlleles` in the lifted VCF I create For example, one record of hg19 is chrom:pos:ref:alt this: `21:11019500:T:C` but lifts over to this: `chr21:10492957:A ...
gatk picard liftover written 17 days ago by curious450
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Comment: C: Allele frequency calculation for genotype dosage value
... You are going to have to convert those dosages to "hard calls", like by rounding to the nearest 0,1,or2. These rounded values can be used to calculate allele frequency ...
written 24 days ago by curious450
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Answer: A: Microarry (GSA) manifest file and CytoSNP-850K manifest file comparison
... You should be able to get the manifests from illumina and you will either have to code up the bit to compare rsids in r or python or try to figure it out in excel. ...
written 24 days ago by curious450
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Answer: A: Why different reference panels change the signal for a SNP?
... I can't see your paper, its behind a paywall but is it just showing better signal in association from imputing with HRC? Take a look at that second link what are the big differences between hapmap and HRC? Also take a look at the benefits section of the HRC website, might give you some clues: h ...
written 28 days ago by curious450
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Comment: C: Switch ref/alt alleles vcf file
... I cant find too much documentation on this flipping from a list, the steps here are not super clear. I know how to flip ref alt in python, but I would like to be able to do it in bcftools for speed. 1. Its not really clear what you mean by list, but have used bcftools annotate before. Do you mean j ...
written 4 weeks ago by curious450
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How does beagle get phase for sites that are NOT in the reference panel
... Im doing some phasing and genotype imputation of a target data set using a reference panel and Beagle. The way I understand it the phase of the target sites that overlap with the panel are going to be inferred by using the phase of the reference panel, beagle then imputes sites to the target based ...
imputation phasing beagle written 4 weeks ago by curious450
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Answer: A: Does 1000 genomes have a flat file with allele frequencies for each site anywher
... Its here: wget -O af.vcf.gz ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz ...
written 5 weeks ago by curious450
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Comment: C: B allele frequency (BAF)
... B allele frequency, like from a illumina genotyping array? ...
written 5 weeks ago by curious450

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