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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 in "snpgdsVCF2GDS_R" function is…
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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 ALT QUAL FILTER INFO FORMA…
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---
Author Name: **Albert Vilella** (Albert Vilella)
Original Redmine Issue: 2078, https://redmine.open-bio.org/issues/2078
Original Date: 2006-08-17
Original Assignee: Bioperl Guts
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I think it …
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Hi,
I get an error when I'm trying to convert from a vcf file to a gds file using the SeqArray package. Here is my code and the error message.
gds.file
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Iterators should be able to yield `var`'s.
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Hello, I am trying to use seqVCF2GDS and am getting the following error:
library(SeqArray)
library(data.table)
seqVCF2GDS(high_mod_vcf, "r4_chr1_high_mod.gds", parallel=6L)
Mon Nov 6 16:09:0…
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La función computeRecombProbabilities_inFile me ha dado el siguiente error:
```
res traceback()
2: CgetIndexfromGenCoord(gds_file, seqlevels(range), start(range),
end(range), 0.1)
1: c…
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Hi @zhengxw-ab
I am interested to create GDS file using VCF from imputed data. I would like to keep dosage information intact in this process.
I use command as:
`
seqVCF2GDS("CHR22.recode.vcf…
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Hi, amazing resource of tools built here!
I have a question regarding the seqParallel function. I can see the `cl` arguement takes a BiocParallelParam object. I attempted to use it with a [Batchtoo…