User: epifaniarango

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Posts by epifaniarango

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Format error with EIGENSOFT
... Hi everyone! I just download a dataset form the David Reich web (https://reich.hms.harvard.edu/sites/reich.hms.harvard.edu/files/inline-files/NathanN_Data_forRelease_Patagonia.zip). I am trying to convert it to PLINK format which I am more familiar with using convertf with the following par file. ...
eigensoft genome snp written 2 days ago by epifaniarango0
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Error while running Beagle for imputation
... Hi everyone! I am trying to run Beagle for imputation. My script is this one: java -jar $Beagle_jar gt=/srv/kenlab/epifania/GelatoHO_dataset/GelatoHO_by_chr/GelatoHO_1.vcf.gz ref=/srv/kenlab/epifania/GelatoHO/phased_no_ref_panel/phased_no_ref_panel_1.filterNOalt.vcf map=/srv/kenlab/epifania/G ...
vcf software error beagle snp genome written 8 months ago by epifaniarango0 • updated 8 months ago by Kevin Blighe63k
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Problems with Reference alleles at VCF files
... Hi! I am having big issues with my vcf files. Some of the SNPs are no variable but instead of having 'N' as value for missing data, my files have a '.' which doesn't allow me to run Beagle. Do you know an easy way to change the missing reference allele to 'N'? Thank you so much for your help =) ...
vcf reference snp written 9 months ago by epifaniarango0

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