User: curious

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curious320
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Posts by curious

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Lifting over and harmonizing a plink file so major allele is forward on hg19?
... I got a PLINK file from a publication. I want to have the major allele correspond to the forward strand of hg19 because I want to analyze it with another file that is organized in this manner. I am curious if this is possible and if my thinking below is the right way. Here is the head of the bim fi ...
strand plink liftover written 2 days ago by curious320
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Comment: C: Imputation output from TOPMED server
... 1- The output of the imputation does it contain typed and untyped SNPs ? - This question is worded a little strange, but should contain both if I understand your ask right. open the "info" file that comes with the download to see which sites were typed only (not in the reference panel) or typed an ...
written 3 days ago by curious320
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Using only non-reference homozygous sites to evaluate SNP array concordance?
... I am checking genotyping concordance by using the same sample genotyped multiple times on the same illumina SNP array. Someone recommended that I only look at non-reference homozygous sites for concordance. I have seen some mentions of this online, but to no real explanation for why this would be us ...
snp array written 3 days ago by curious320
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Comment: C: Setting major allele in plink to plus strand of reference?
... Ill give it a shot, thanks I was really scratching my head over this. ...
written 3 days ago by curious320
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Setting major allele in plink to plus strand of reference?
... I have a plink file that someone gave me. I wan't to use it in an analysis where I know that the major allele needs to be set to the plus strand of the GRCh37 assembly. I try: `plink2 --bfile {my_fav_file} --make-bed --ref-from-fa --fa {ref_fa} --out {my_fav_file_new}` I get: `Error: Unrecognize ...
plink written 4 days ago by curious320
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Comment: C: Possible to add `chr` prefix to each chromosome in PLINK?
... Thank you, the MT code threw me off a bit, I didn't know it would affect all chromosomes.`--output-chr ` ...
written 12 days ago by curious320
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Possible to add `chr` prefix to each chromosome in PLINK?
... I have a small plink file and a very large VCF that I need to use as input for an analysis. The analysis needs the chrom designations in these files to be the exact same. The VCF have 'chr' prefix in the #CHROM col. I know how to change this in the VCF, but it sets back my pipeline several days. I ...
plink written 12 days ago by curious320 • updated 12 days ago by chrchang5237.1k
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Comment: C: How to add a flag to the INFO column of a vcf with pysam?
... I figured it out: vcf_in = VariantFile("chr22.vcf") vcf_in.header.add_meta('INFO', items=[('ID',"IMPUTED"), ('Number',0), ('Type','Flag'), ('Description','Marker was imputed')]) for counter, rec in enumerate(vcf_in.fetch('chr22', 10510227, 10540227)): rec.info.__setitem__(' ...
written 15 days ago by curious320
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How to add a flag to the INFO column of a vcf with pysam?
... so for info content of a vcf I know I can set key value pairs like this: vcf_in = VariantFile("chr22.vcf") for counter, rec in enumerate(vcf_in.fetch('chr22', 10510227, 10540227)): rec.info["MAF"] = whatever But I want to add something at `Type=Flag`, the flag `IMPUTED` to be ...
vcf bcf pysam written 16 days ago by curious320
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Comment: C: Extracting strings from the fasta header
... Split/focus on the actual keys like `locus-tag` or `location=compliment` if those are consistent. This might require regular expressions ...
written 18 days ago by curious320

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Scholar 8 weeks ago, created an answer that has been accepted. For A: conda/bioconda installation of plink fails
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Scholar 4 months ago, created an answer that has been accepted. For A: conda/bioconda installation of plink fails
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