R, package: ldblock, function stack1kg error in opening BCFFile
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ting835698 • 0
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Last seen 3 days ago

I am trying to get a VCF stack from the 1000 genome project using package "ldblock" on R (version 4.0.3), but when I used function

sta = stack1kg()


the following error was shown.

Error in open.BcfFile(BcfFile(file, character(0), ...)) : 'open' VCF/BCF failed filename: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/ALL.chr1.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz

I tried stack1kg(chrs = as.character(1:22)) and manually change the number from 1 to 22, all shown similar message as above (the only thing that changed was the filenames). So I assumed it is caused by missing package(s). I downloaded Rsamtools, VariantAnnotation, updated xfun, GenomicFiles and some others, none seems to work.

I dont know whether the material I am learning from is a bit too old (the last update is in 2017) , does everyone still using ldblock to obtain VCF stacks? If anyone had experienced something similar to this or if there is a solution pls let me know. Many Thanks.

ldblock • 23 views