Moderator: chrchang523

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chrchang5236.5k
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Posts by chrchang523

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Answer: A: plink2 extract subset of samples from .bgen file
... plink2 \ --bgen <.bgen filename> ref-last \ --sample <.sample filename> \ --keep \ --export bgen-1.3 \ --out Note that this only preserves dosages, not genotype probabilities. If you care about preserving the raw probabilities in the .bgen file, you ...
written 22 hours ago by chrchang5236.5k
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Answer: A: ld-pruning to a specific number of SNPs
... This is not directly supported, but you can achieve the same effect by choosing an appropriate window size/r2 which yields slightly more SNPs, and then following up with `plink --bfile --thin-count 1000000 --make-bed --out ...`. ...
written 6 days ago by chrchang5236.5k
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Comment: C: How to read a ".ld.bin" file produced by PLINK
... I have added a link under the .ld file format documentation to a sample readBin() call; let me know if this is still insufficient. ...
written 7 days ago by chrchang5236.5k
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Answer: A: Tool to check what alternate allele is dominant across samples per line of the V
... With plink 2.0, `plink2 --vcf --freq counts` gets this information for you. (Remove 'counts' if you want proportions instead.) ...
written 7 days ago by chrchang5236.5k
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Comment: C: update-chr issues with PLINK 1.9
... As explained in the documentation, —output-chr’s argument is the mitochondrial code, since that changes the most between datasets. ...
written 9 days ago by chrchang5236.5k
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Comment: C: how to count variants par sample per chromosome in a vcf file?
... What happens if you add —make-pgen to the first command line? ...
written 9 days ago by chrchang5236.5k
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Answer: A: update-chr issues with PLINK 1.9
... plink 1.9 treats the chromosome codes “23” and “X” as interchangeable, but for backward compatibility it defaults to outputting the numeric form. Use —output-chr (https://www.cog-genomics.org/plink/1.9/data#irreg_output ) to change this for a specific run. Note that plink 2.0 outputs X instead of ...
written 9 days ago by chrchang5236.5k
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Comment: C: Plink Error in PCA plot
... That isn’t the entire .log file, but it’s enough. Why do you expect this to work? The file contains only one sample, not 70. ...
written 13 days ago by chrchang5236.5k
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Comment: C: Plink Error in PCA plot
... Please post the entire .log file. ...
written 13 days ago by chrchang5236.5k
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Answer: A: how to use plink to get all the SNP LD score > 0.8 in matrix format?
... If you want a matrix with all values > 0.8 set to zero, just write a one-line postprocessing script that replaces values <= 0.8 with zero. ...
written 15 days ago by chrchang5236.5k

Latest awards to chrchang523

Teacher 23 days ago, created an answer with at least 3 up-votes. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Good Answer 4 weeks ago, created an answer that was upvoted at least 5 times. For A: How to I convert 23andMe Raw Genome to GenBank or FASTA?
Appreciated 5 weeks ago, created a post with more than 5 votes. For A: Weir And Cockerham Fst from PLINK(bed/bim/fam) input files
Scholar 5 weeks ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Appreciated 6 weeks ago, created a post with more than 5 votes. For A: Weir And Cockerham Fst from PLINK(bed/bim/fam) input files
Scholar 6 weeks ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Scholar 7 weeks ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Scholar 9 weeks ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Scholar 10 weeks ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Scholar 10 weeks ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Scholar 10 weeks ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Scholar 11 weeks ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Scholar 12 weeks ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Scholar 3 months ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Scholar 3 months ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Scholar 6 months ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: How to I convert 23andMe Raw Genome to GenBank or FASTA?
Appreciated 7 months ago, created a post with more than 5 votes. For A: Weir And Cockerham Fst from PLINK(bed/bim/fam) input files

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