User: gary.napier

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Posts by gary.napier

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Quick way of returning list of positions from vcf file with bcftools query
... Thanks for the suggestion, but it doesn't seem to be any quicker unfortunately. My file is huge, so I guess this is to be expected! ...
written 3 days ago by gary.napier0
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Quick way of returning list of positions from vcf file with bcftools query
... Hi, Is there a quicker way of extracting the number of positions from a vcf file using bcftools query? When I run `bcftools query -l .vcf.gz | wc` it returns the list/number of samples very rapidly, however when I run `bcftools query -f '%POS\n' .vcf.gz | wc` as stated here: https://samtools.git ...
vcf bcftools written 3 days ago by gary.napier0
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Comment: C: What is the relationship between PLINK --pca and --mds-plot in terms of % varian
... I see, thank you. So when I call `--mds-plot 10`, does this return a compression of the data into just 10 components, or is it outputting a truncated list of *as many components as there are variables* (as you would expect from a conventional PCA)? In other words is `--mds-plot 10` doing the anala ...
written 10 days ago by gary.napier0
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What is the relationship between PLINK --pca and --mds-plot in terms of % variance explained
... Hi, I am trying to get the correct percent of variance explained by a PLINK PCA analysis (--mds-plot). When I run the code with a parameter of 10 PCAs... plink --vcf --mds-plot 10 eigendecomp --cluster --double-id --allow-extra-chr --out ...as expected I get ten columns (C1 - C10). The ...
eigenvalues pca mds plink written 10 days ago by gary.napier0 • updated 10 days ago by h.mon29k
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Answer: A: How to pass a variable to vcftools --weir-fst-pop
... This seems to work: `vcftools --bcf --weir-fst-pop <(echo ${}) --weir-fst-pop <(echo ${}) ` ...
written 19 days ago by gary.napier0
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How to pass a variable to vcftools --weir-fst-pop
... Is it possible to pass a population list as a variable to the `vcftools --weir-fst-pop` function instead of a file? My original code is correct and works: `vcftools --bcf --weir-fst-pop --weir-fst-pop --out ` However I need to run this code many times in a loop and it would be preferable not to ...
fst vcftools bash written 19 days ago by gary.napier0
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Comment: C: bcftools view error: "F_PASS" is not defined in the VCF header
... Thank you! It worked. ...
written 27 days ago by gary.napier0
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Comment: C: bcftools view error: "F_PASS" is not defined in the VCF header
... Hi, I am using bcftools 1.7 (Using htslib 1.7-2). ...
written 27 days ago by gary.napier0
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Comment: A: bcftools view error: "F_PASS" is not defined in the VCF header
... I am using bcftools 1.7 (Using htslib 1.7-2). ...
written 27 days ago by gary.napier0
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bcftools view error: "F_PASS" is not defined in the VCF header
... When I run this command: ```bcftools view -i 'F_PASS(GT!="mis")>0.9' ``` I get this error: ```Error: the tag "F_PASS" is not defined in the VCF header``` My command seems to follow the syntax in the example on this page: http://samtools.github.io/bcftools/bcftools.html where it is stated as ` ...
bcftools written 27 days ago by gary.napier0

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