Question: Error converting vcf to gds
0
gravatar for annat22
13 months ago by
annat220
annat220 wrote:

Hello,

I keep having an error converting vcf to gds with SNPRelate. I got the same error with two different ones, although it worked fine with other datasets previously. Pasted below is the code and error msg with session info. It basically says there are fewer columns than what expected. I re-ran everything up to this point to make sure the vcf is ok, and I can query it with bcftools with no issues, so it doesn't look like the vcf file is corrupted.

Would greatly appreciate any input.

Annat

> snpgdsVCF2GDS("Joint_allSNPjointMAF05.vcf.gz", "Joint_allSNPjointMAF05.gds", method="biallelic.only")

VCF Format --> SNP GDS Format

Method: exacting biallelic SNPs

Number of samples: 1894

Parsing "Joint_allSNPjointMAF05.vcf.gz" ...

Error:

FILE: Joint_allSNPjointMAF05.vcf.gz

    LINE: 1615045, COLUMN: 1605, 0/0:.:32,0:32:0:.:.:0,0,571

    fewer columns than what expected.

> traceback()

2: .Call(gnr_Parse_VCF4, vcf.fn[i], gfile$root, metidx, readLines,

       opfile, 1024L, ref.allele, ignore.chr.prefix, new.env(),

       verbose)

1: snpgdsVCF2GDS("Joint_allSNPjointMAF05.vcf.gz", "Joint_allSNPjointMAF05.gds",

       method = "biallelic.only")

>

> #snpgdsVCF2GDS("../../../../Raw/1000G/1000Genome_calls_all_chromosomes.vcf.gz","1000G_allSNPjointMAF05.gds", method="biallelic.only")

>       

> #snpgdsCombineGeno(c("Joint_allSNPjointMAF05.gds", "1000G_allSNPjointMAF05.gds"),

>  #       "Joint1000G_allSNPjointMAF05.gds")

> sessionInfo()

R version 3.1.1 (2014-07-10)

Platform: x86_64-unknown-linux-gnu (64-bit)

 

locale:

[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              

[3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    

[5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   

[7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 

[9] LC_ADDRESS=C               LC_TELEPHONE=C            

[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

 

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base     

 

other attached packages:

[1] SNPRelate_1.0.1 gdsfmt_1.2.2   

snprelate vcf gds • 311 views
ADD COMMENTlink modified 13 months ago by zhengx20 • written 13 months ago by annat220
Answer: Error converting vcf to gds
0
gravatar for Stephanie M. Gogarten
13 months ago by
University of Washington
Stephanie M. Gogarten600 wrote:

Your version of R is nearly 4 years out of date. Please upgrade to current R and Bioconductor package versions and try again.

ADD COMMENTlink written 13 months ago by Stephanie M. Gogarten600
Answer: Error converting vcf to gds
0
gravatar for zhengx
13 months ago by
zhengx20
United States
zhengx20 wrote:

You might try SeqArray::seqVCF2GDS(), which could provide you more error information.

 

ADD COMMENTlink written 13 months ago by zhengx20
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