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Dear developer(s),
I wonder if there is any chance to get a gds (or vcf) file once a snp dataset (with multiple samples inside) has been pruned. Unfortunately I am not an R expert but it seems snpg…
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Dear @zhengxwen / @zhengxw-ab ,
Hope you are keeping well.
I was trying to merge two samples:
`seqMerge(c("sample_1.gds", "sample_2.gds"), "merged.gds", storage.option="LZMA_RA", verbose=TRUE))…
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Hi,
I've used SeqArray::seqVCF2GDS to convert a haploid species VCF v4.2 file to gds format which has variants with multiple alternative alleles due to the nature of our sequencing which involves s…
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Hi, this is a great idea, and really useful package. 2 quesions:
1. I note from the README.md that this package is "based on the original SAIGE package (v0.29.4.4)". But I'm not certain if that me…
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```
Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.3 (2024-02-29)
Installing package(s) 'SeqArray'
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/SeqArray_1.42.3.tar.gz…
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Background: I've used imputedDosageFile to get my Beagle output in a format I can use with SeqArray. Then I used seqSNP2GDS to make a file for use with SeqVarTools. This object only includes dosage …
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Dear Sir
Now I am learning to use SeqArray package.
I am trying to use the package to convert my Exome VCF SNP file into SNPGDS file for SNPrelate package for analysis relatedness.
I use `seqVCF2GD…
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Some variants in SeqArray gds files can have multiple alternate alleles. I looked into how the LD functions behave with multiallelic variants using the example file in [analysis_pipeline](https://gith…
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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