User: karl.fetter

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Posts by karl.fetter

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Comment: C: bcftools merge deleting all genotypes from second file
... > ALL ? can you confirm this ? Thanks for the suggestion, I can confirm this. I looked closer at the file and while both input files are 85K loci large, the output is 171K. What is happening is that the two files are being concatenated and sites in file2 are set to unknown in the top half, and s ...
written 2.8 years ago by karl.fetter0
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bcftools merge deleting all genotypes from second file
... Hello All, I'm trying to merge 2 vcf.gz files and I'm running into a strange behavior using bcftools merge. All of the positions in my second file are being setting to missing (./.) during the merge. Does anyone have any tips for how I might fix this problem? Here is my command: ```bcftools merge ...
merge bcftools written 2.8 years ago by karl.fetter0
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Beagle Error Reading in .PL file
... Hello Biostars, I am attempting to use beagle to impute missing genotypes. I created a .PL file containing genotypes and likelihood scores for the genotypes using vcftools. I created a single file for each chromosome and named them chr1.BEAGLE.PL, chr2.BEAGLE.PL, etc. I used the following command t ...
genome phasing beagle written 3.6 years ago by karl.fetter0

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