zhengxwen SeqArray issues

zhengxwen / SeqArray

Data management of large-scale whole-genome sequence variant calls (Development version only)

http://www.bioconductor.org/packages/SeqArray

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issues

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Error in seqExport(genofile, gdsfile_filtered) : Not implemented in 'genotype/extra.index', please contact the author.

#97 maitree-patel opened 2 months ago
0
Flipped $ref and $alt when converting plink binary files to gds format

#96 ryshi06 opened 2 months ago
2
The +1 problem - adding new samples incrementally

#95 boboppie opened 3 months ago
0
All genotypes in gds format are NA!

#94 MiladEidi closed 4 months ago
0
seqMerge error - File 2: chromosomes and positions are unsorted.

#93 boboppie opened 5 months ago
2
Error in seqVCF2GDS(vcf.fn, "chr1.gds", storage.option = "LZMA_RA", parallel = FALSE) : std::bad_alloc

#92 LiuYuMeng987654 opened 6 months ago
1
seqMerge error

#91 davidroberson closed 5 months ago
6
seqMissing with per.variant=FALSE returns empty vector

#90 smgogarten closed 7 months ago
1
SeqArray-1.42.3 build fails with R-4.3.3 and GCC 13.2.0

#89 fizwit opened 8 months ago
4
The package does not install with the LLVM 17 compilers

#88 lhe17 opened 8 months ago
1
Sample.idError with seqVCF2GDS

#87 alexisregelson opened 1 year ago
3
how to give ploidy a non missing value in a dosage data set

#86 nickychapman opened 1 year ago
3
Invalid variant dimension in 'genotype/data' and Ploidy=1 with more than 2 alleles per variant

#85 gtollefson opened 1 year ago
8
Invalid position in C Index

#84 dylanHco closed 1 year ago
2
SeqAlleleCount issue with unused argument (.progress = TRUE)

#83 leoneago closed 2 years ago
1
How to save converted file

#82 manburst opened 2 years ago
2
error when running seqVCF2GDS

#81 maxineliu opened 2 years ago
1
seqSetFilter(, variant.sel=..., ret.idx=TRUE)

#80 zhengxwen closed 2 years ago
1
seqAlleleCount returns NA if no samples in filter

#79 smgogarten closed 2 years ago
2
seqGetData genotype with wrong genotype on multiallelic sites

#78 no7ren closed 2 years ago
2
Bug :Stream Error with seqSetFilterAnnotID ( I supposed)

#77 iaia87 closed 2 years ago
5
Error in seqVCF2GDS(vcf.files, gds.file, verbose = FALSE)

#76 Bulouere opened 2 years ago
1
Installation problems

#75 laiajulianamu opened 2 years ago
2
Problem in SeqArray::seqVCF2GDS - Parsing the vcf header fails

#74 iaia87 opened 2 years ago
2
Estimating IBD using MLE

#73 BELKHIR opened 3 years ago
3
SeqAddValue Invalid varnm

#72 gustavahlberg closed 3 years ago
0
Create GDS file from imputed data using dosage || No variable 'annotation/format/DS' in the FORMAT field.

#71 complexgenome opened 3 years ago
2
Missing VCF INFO field causes seqVCF2GDS error

#70 kaskarn closed 3 years ago
1
PCs are all NA when number of samples >50K

#69 jjfarrell closed 3 years ago
1
seqGDS2VCF error after using seqMerge

#68 gustavahlberg opened 3 years ago
8
error:

#67 yangli-ai closed 3 years ago
2
seqParallel with BiocParallel::BatchtoolsParam object ?

#66 ldcato opened 4 years ago
2
SeqArray reading problem with vcf from samtools

#65 thierrygosselin closed 4 years ago
1
seqBED2GDS switches REF and ALT alleles

#64 smgogarten closed 3 years ago
3
seqBED2GDS fails if "#" character is present in variant identifier

#63 smgogarten closed 4 years ago
1
how to creat an empty SeqArray GDS file

#62 terrryliu closed 4 years ago
6
PLINK bed file conversion switch the variant and sample

#61 thierrygosselin closed 4 years ago
1
Problem in VCF AD field imported by SeqArray

#60 thierrygosselin closed 4 years ago
4
seqBlockApply() is unexpectedly slow for "annotation/info/VARIABLE"

#59 zhengxwen closed 4 years ago
1
seqGetData(, "genotype", .useraw=NA) not work?

#58 zhengxwen closed 4 years ago
1
Duplicate indices in `seqSetFilter(f, variant.sel=)`

#57 zhengxwen closed 5 years ago
0
Should seqSetFilter() use the same data type as input for `sample.id` and `variant.id`??

#56 zhengxw-ab closed 5 years ago
0
error: could not find function "seqVCF2GDS"

#55 lakishadavid closed 5 years ago
1
Importing DArT file and converting to VCF

#54 pezhmansafdari closed 4 years ago
1
Suggestion: seqVCF2GDS could use index file to get total number of variants

#53 jemunro opened 5 years ago
0
genotypes have been called in haploid mode, they don't have a phase

#52 JiruHan closed 5 years ago
2
Changing genotypes

#51 thierrygosselin closed 5 years ago
2
Empty GDS

#50 thierrygosselin closed 5 years ago
1
commit 636df92 breaks creation of SeqVarData objects

#49 smgogarten closed 5 years ago
0
potential bug with SeqArray

#48 thierrygosselin closed 5 years ago
9