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How to quickly tell the reference allele given chr, pos, A1 and A2 allele?

ref allele reference allele snp written 8 months ago by Tao • 420

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Is there a FASTA file containing 1000 Genomes variant information to check reference alleles in VCF files?

1000 genomes reference allele checkvcf written 20 months ago by rodd • 130 • updated 19 months ago by chrchang523 ♦ 7.6k

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Where to download official reference and alternative alleles from 1000 Genomes?

1000 genomes reference allele plink written 2.9 years ago by Mr Locuace • 100 • updated 2.9 years ago by chrchang523 ♦ 7.6k

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Should I assume that the genotype of the 1000 Genomes project individuals in positions that are not in the vcf file, are homozygous for the reference allele?

vcf reference allele 1000 genomes project written 3.6 years ago by magda • 20

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How to create reference allele file in plink? (~50 SNPs)

impute2 reference allele plink written 5.6 years ago by eyb • 190

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Recent Replies

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If external libraries are an option, I'd recommend trying Kevin Blighe's EnhancedVolcano package....
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None of the above :-) If you click on the user name you can see when they last logged in.
C: Human snoRNA atlas from small RNA sequencing data in deepBase by joe • 170
Thanks GenoMax, are you a bot/AI or just omnipresent? (which is almost the same)
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Linux has been successfully ported to M1: https://corellium.com/blog/linux-m1
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This user has not logged in to Biostars for over a year so think of a plan B, just in case.
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Hey SnoSeekerNGS devs - in case you're still around, is there any chance this package is still ma...
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depends on what exactly you want to achieve but yes, `agat_sp_merge_annotations.pl` sounds about ...
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I think you can do step 2 with a little preprocessing also, but depending on the size of your net...
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Use --make-pgen/--pfile instead of --make-bed/--bfile when working with multiallelic variants.
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From https://www.cog-genomics.org/plink/1.9/filter#thin : "--thin removes variants at random by r...
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They will usually be left in the dataset, even after normalisation. However, these probes should ...

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