Closed iaia87 closed 2 years ago
I create my gds file again and I solve my problem in this manner. I think that in filtering I have not closed some files and this cause my problem.
I have an other question, I want to merge files gds, after filtering by variants, but I have had to create new vcf, because I have not found how to merge on filtered files with SeqArray and SeqVarTools does not propose such option.
If you can help on this subject, I will be very grateful !
Best regards, Laura
You have to create the filtered GDS files, before merging.
Hi,
Thanks a lot for your help ! To create filtered gds, I create a filtered vcf and after that I trasform them in filtered gds, do you know if I can do this in an other way ?
I begun to use your package and I do not find an other strategy, without loosing imputation information.
Best regards, Laura
Le ven. 3 juin 2022 à 00:14, Xiuwen Zheng @.***> a écrit :
You have to create the filtered GDS files, before merging.
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You can use seqExport()
to export a filtered GDS file to a new GDS file, which is used in merging later.
seqSetFilter()
can be used to set a filter on the GDS file.
Thanks a lot for your help, I don't know why I though that this commande create a gdsfile for SNPRelate and not for seqArray...
Thanks a lot !
Laura Lombardi
Le ven. 3 juin 2022 à 23:33, Xiuwen Zheng @.***> a écrit :
You can use seqExport() to export a filtered GDS file to a new GDS file, which is used in merging later.
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Hello,
I have many .gds files. I had obtained a stream error today and I totally blocked !
I supposed that the problem come from my setFilter, but I am not sure and I completely blocked now... Any idea to resolve ?
Have you some better idea to obtain a gds by filtering on variants without creating a new vcf ?
Here you are my code :
names <- 0 for (i in 1:22) { names[i]<-paste0("chr", i) } names
gds_list_GWAS1_EUR <- list() out_GWAS1_EUR.fn <- list()
for (i in 1:length(names)) { gds_list_GWAS1_EUR[[i]] <- c( paste0("/media/lauraNFS3/Laura_ConLiGen/POST_IMPUTE_DATA_V2/gds_file/chr",i,"-GWAS1_1million_hg19.gds"), paste0("/media/lauraNFS3/Laura_ConLiGen/POST_IMPUTE_DATA_V2/gds_file/chr",i,"-GWAS1_GAIN_hg19.gds"), paste0("/media/lauraNFS3/Laura_ConLiGen/POST_IMPUTE_DATA_V2/gds_file/chr",i,"-GWAS1_HAP610_hg19.gds"), paste0("/media/lauraNFS3/Laura_ConLiGen/POST_IMPUTE_DATA_V2/gds_file/chr",i,"-GWAS1_HAP660_part1_hg19.gds"), paste0("/media/lauraNFS3/Laura_ConLiGen/POST_IMPUTE_DATA_V2/gds_file/chr",i,"-GWAS1_Omni2.5_EUR.gds"), paste0("/media/lauraNFS3/Laura_ConLiGen/POST_IMPUTE_DATA_V2/gds_file/chr",i,"-GWAS1_Omni_express_EUR.gds")) out_GWAS1_EUR.fn[[i]] <- paste0("/media/lauraNFS3/Laura_ConLiGen/POST_IMPUTE_DATA_V2/gds_file/chr", i, "-GWAS1_EUR_def.gds") names(gds_list_GWAS1_EUR)[[i]] <- names[i] names(out_GWAS1_EUR.fn)[[i]] <- names[i] } out_vcf_filtred.fn <- list()
for (i in 1:length(names)) { out_vcf_filtred.fn[[i]] <- c( paste0("/media/lauraNFS3/Laura_ConLiGen/POST_IMPUTE_DATA_V2/gds_file/chr",i,"-GWAS1_1million_hg19.gds"), paste0("/media/lauraNFS3/Laura_ConLiGen/POST_IMPUTE_DATA_V2/vcf/filtred-chr",i,"-GWAS1_GAIN_hg19.vcf.gz"), paste0("/media/lauraNFS3/Laura_ConLiGen/POST_IMPUTE_DATA_V2/vcf/filtred-chr",i,"-GWAS1_HAP610_hg19.vcf.gz"), paste0("/media/lauraNFS3/Laura_ConLiGen/POST_IMPUTE_DATA_V2/vcf/filtred-chr",i,"-GWAS1_HAP660_part1_hg19.vcf.gz"), paste0("/media/lauraNFS3/Laura_ConLiGen/POST_IMPUTE_DATA_V2/vcf/filtred-chr",i,"-GWAS1_Omni2.5_EUR.vcf.gz"), paste0("/media/lauraNFS3/Laura_ConLiGen/POST_IMPUTE_DATA_V2/vcf/filtred-chr",i,"-GWAS1_Omni_express_EUR.vcf.gz")) names(out_vcf_filtred.fn)[[i]] <- names[i] }
id <- mcols(Conligen_granges$chr22)$SNPs_ID
genofile_chr22 <- list() for (i in 1:6) { genofile_chr22[[i]] <- seqOpen(gds_list_GWAS1_EUR[[22]][i]) }
unitil now, it's OK !
for (i in 1:6) { seqSetFilterAnnotID(genofile_chr22[[i]], id, ret.idx=FALSE, verbose=TRUE)} # no problem
for (i in 1:6) { seqGDS2VCF(genofile_chr22[[i]], out_vcf_filtred.fn[[22]][i], info.var=NULL, fmt.var=NULL, chr_prefix="", use_Rsamtools=TRUE, verbose=TRUE) }
First Stream Error
I quit and now, if I pass the command of seqOpen, I obtain : Stream Read Error, need 12 byte(s) but receive 0
Sorry, if it a bit long... I hope that you can help me !
Thanks a lot, Laura