SNPRelate
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zhengxwen
R package: parallel computing toolset for relatedness and principal component analysis of SNP data (Development version only)
I'm starting to get an error when running seqVCF2GDS function to covert BCFTools, Strelka2 and GATK uncompressed VCF to GDS. The code i'm using: gatkgds
Hi, When I run the code below, `library("SNPRelate")` `snpgdsVCF2GDS("xxxx.vcf", "ccm.gds", method="biallelic.only")` `genofile
Hi, I am working on variant analysis of organelle genome but I could not make sure If I use my output files in SNPRelate for this purporse. Because method parameter...
Hi, I was using the snpgdsLDpruning function to determine the actual number of independent SNPs in my genotype file, to perform BF correction for my GWAS. The function gives me...
In the example given in your document, the data used was a human genome. Can SNPRelate be used to analysis Plasmodium falciparum snp data as well?
Dear Xiuwen Zhen I've imported a vcf file, using snpgdsVCF2GDS, with SNPs for 10 samples, which looks like this: ## (lots of comment lines) ## (...) #CHROM POS ID REF...
We are getting an error when our sample size goes above 50,000. The PC-AIR step results in just NAs for all the PCS. At 45k samples, it runs fine. Originally...
Hi - It looks like the snpgdsCombineGeno function does an intersection and only retains the common SNPs. Is it possible to do a union of all GDS files? Thanks for...
Hello, I am working on a PCA analysis of some populations for a conservation genetics project on a crayfish species. My DAPC analysis did not show significant structure between sites,...
In SeqArray object, this is variant.id. When SNPRelate::snpgdsSummary( ) opens SeqArray object, it gives error: Error in index.gdsn(gds, "snp.id") : No such GDS node "snp.id"!. How to link snp.id to...
