User: chrchang523

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chrchang5232.2k
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Posts by chrchang523

<prev • 230 results • page 1 of 23 • next >
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Comment: C: how to switch REF and ALT alleles in VCF files if the REF is incorrect according
... It depends on what your RefSeq file looks like. The basic structure of the command would be plink --vcf [name of plink-exported VCF with incorrect reference alleles] --a2-allele [name of RefSeq file] [1-based column index of ref alleles] [1-based column index of variant IDs] --recode vcf --rea ...
written 3 days ago by chrchang5232.2k
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Answer: A: how to switch REF and ALT alleles in VCF files if the REF is incorrect according
... Given a file with the correct reference alleles for each variant ID, you can use plink's --a2-allele flag to fix them in the VCF. ...
written 3 days ago by chrchang5232.2k
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Answer: A: Get LD data for any two SNPs
... "plink --r2 in-phase" provides both r-squared and directionality; see https://www.cog-genomics.org/plink/1.9/ld#r . ...
written 5 days ago by chrchang5232.2k
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Comment: C: plink vcf recodeA error ALT allele duplicates REF allele
... This is because VCF import happens before everything else plink does: the entire file is imported, and only then are flags like --maf applied. Otherwise, it would be necessary to add --maf logic to every single import routine, etc. (The full order of operations is at https://www.cog-genomics.org/p ...
written 13 days ago by chrchang5232.2k
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Answer: A: plink vcf recodeA error ALT allele duplicates REF allele
... How was this VCF file generated? The REF and ALT alleles should never be identical; monomorphic variants should have either "." or some unobserved alternate allele in the ALT column. With that said, you can recover from this situation with a script that detects lines where the REF and ALT columns ...
written 13 days ago by chrchang5232.2k
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Answer: A: Obtain alleles A1 and A2 alleles from plink output
... With plink 1.9, assuming that the A2 alleles in chrom##.bim are always major (you can double-check by running "./plink --bfile ../cal/chrom## --make-bed" and verifying that the new .bim file is identical to the old one, since plink 1.x automatically flips minor A2 alleles), you can 1. Create an all ...
written 21 days ago by chrchang5232.2k
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Comment: C: Inconsistency in VCF and Plink format after conversion
... Can you be more specific about an additional problem you're having with 1.9? I'm actively updating it to remove problems with replacing v1.07 with v1.9 (and this is now the only way in which v1.9 is updated; all new stuff is only going into the v2.0 codebase at this point). ...
written 4 weeks ago by chrchang5232.2k
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Comment: C: Inconsistency in VCF and Plink format after conversion
... Does this work if you use plink for the import instead (e.g. "plink --vcf myfile.vcf.gz --recode --out myfile_plink")? ...
written 4 weeks ago by chrchang5232.2k
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Comment: C: use of 2 covariate files for association analysis in plink
... With a bash script: A. Merge the FID and IID fields with something like cat orig_covar_1.txt | awk '{out=$1"_"$2; for(i=3;i<=NF;++i){out=out"\t"$i}; print out}' > covar_merged_ids_1.txt cat orig_covar_2.txt | awk '{out=$1"_"$2; for(i=3;i<=NF;++i){out=out"\t"$i}; print out}' > covar_me ...
written 6 weeks ago by chrchang5232.2k
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Answer: A: use of 2 covariate files for association analysis in plink
... No; you'll need to merge the files with a short script. ...
written 6 weeks ago by chrchang5232.2k

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Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
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Scholar 21 months ago, created an answer that has been accepted. For A: Plotting file eigenvec
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