Moderator: chrchang523

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chrchang5234.3k
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Posts by chrchang523

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Answer: A: Convert matrix in numeric format to genotype format
... If your matrix is variant-major (i.e. each line has one variant, each column has one sample), it shouldn't take too much work to manipulate it into a form that plink 2.0 --import-dosage (see http://zzz.bwh.harvard.edu/plink/dosage.shtml for a description of the expected format, and http://www.cog-ge ...
written 7 days ago by chrchang5234.3k
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Comment: C: How to convert a meta-analysis file from PLINK (.meta) to a .csv or.txt to be re
... This is actually a better answer than the one I gave. (I was reposting my reply to the more specific query at https://groups.google.com/forum/#!topic/plink2-users/zbr6cW3LeyU .) ...
written 8 days ago by chrchang5234.3k
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Answer: A: How to convert a meta-analysis file from PLINK (.meta) to a .csv or.txt to be re
... See the comments on converting spaces to tabs under https://www.cog-genomics.org/plink/1.9/other#tabspace . ...
written 8 days ago by chrchang5234.3k
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Comment: C: 1000Genomes population allele frequencies for list of SNPs
... 1. You need to decompress the .pgen.zst file first; see the instructions at the top of the resources page. 2. This requires plink 2.0, not 1.9. What do you get when you type “plink2 —version”? ...
written 9 days ago by chrchang5234.3k
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Answer: A: 1000Genomes population allele frequencies for list of SNPs
... Solution 1: The raw variant call data can be downloaded from http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ . Once you have those files, the INFO column in each VCF file contains superpopulation allele frequencies, and there are a bunch of tools which can look up the INFO column entry ...
written 10 days ago by chrchang5234.3k
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Comment: C: PLINK Error: No valid entries in --score file.
... Use plink 1.9's --gen flag to read your .gen file directly (and --sample to read the .sample). ...
written 18 days ago by chrchang5234.3k
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Answer: A: Count variants between two samples within a multi-sample VCF
... With plink 1.9, `plink --vcf my.vcf --genome full` should provide the necessary counts; add the IBS0 and IBS1 columns to get the total number of differences between two samples. ...
written 18 days ago by chrchang5234.3k
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Answer: A: plink produces does pruning according to log file but prune.in is full of dots
... This is because the `.prune.in` and `.prune.out` files contain variant IDs, but your VCF has all variant IDs set to `‘.’`. plink 2.0’s [--set-all-var-ids flag][1] provides one way to assign IDs. [1]: https://www.cog-genomics.org/plink/2.0/data#set_all_var_ids ...
written 19 days ago by chrchang5234.3k • updated 19 days ago by zx87546.1k
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Comment: C: PLINK --score Erroe
... Check whether any variant IDs and alleles in your —score file exactly match the ones in all.bim. ...
written 21 days ago by chrchang5234.3k
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Answer: A: Find clones in a population using a vcf file.
... With plink 2.0 (https://www.cog-genomics.org/plink/2.0 ): plink2 --vcf ... --make-king-table --king-table-filter 0.354 This uses the KING-robust method (http://people.virginia.edu/~wc9c/KING/manual.html ) to estimated relatedness between each pair of samples. The 0.354 cutoff causes only dupl ...
written 5 weeks ago by chrchang5234.3k

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