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zhengxwen
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SeqArray
Data management of large-scale whole-genome sequence variant calls (Development version only)
http://www.bioconductor.org/packages/SeqArray
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The created BGZF VCF file is truncated
#47
zhengxwen
closed
5 years ago
1
Error in ls.gdsn(node, include.hidden = all) : Stream read error
#46
thierrygosselin
closed
5 years ago
1
get genotypes with nucleotides ?
#45
thierrygosselin
closed
5 years ago
2
fixed asVCF unit test
#44
smgogarten
closed
5 years ago
0
Error message: overlapping on both samples and variants
#43
annaquaglieri16
opened
5 years ago
0
seqGDS2SNP() altering genotype values for haploid data
#42
AAvalos82
opened
5 years ago
1
seqMerge failed because file2 is unsorted
#41
baderd
closed
5 years ago
4
problem with VCF
#40
thierrygosselin
closed
6 years ago
5
seqGDS2VCF() and phasing
#39
AAvalos82
closed
6 years ago
0
update header method for changes in VariantAnnotation 1.27.6
#38
smgogarten
closed
6 years ago
0
Reading subset
#37
zhengxwen
closed
6 years ago
0
problem with SeqArray::seqVCF2GDS
#36
thierrygosselin
closed
6 years ago
5
seqVCF2GDS error in seqVCF_Header
#35
ShawnCone
closed
6 years ago
5
VCF2GDS error with phased VCF files
#34
dtaliun
closed
6 years ago
4
re-calibrate ref/alt allele
#33
thierrygosselin
closed
6 years ago
5
Odd behavior of parallel seqVCF2GDS()
#32
AAvalos82
closed
6 years ago
4
change sample.id in SeqArray
#31
thierrygosselin
closed
6 years ago
1
problem importing very large VCF file
#30
thierrygosselin
closed
6 years ago
3
seqExport() fails for data with ploidy 1
#29
jemunro
closed
6 years ago
4
seqGDS2VCF does not generate a bgzip vcf file
#28
trb8
closed
6 years ago
1
inconsistent behavior with seqSetFilter
#27
smgogarten
closed
6 years ago
1
segmentation fault after setting filter to 0 variants
#26
smgogarten
closed
6 years ago
0
fix for 'missing file link' errors in check
#25
smgogarten
closed
6 years ago
0
initialize C library .onLoad rather than .onAttach
#24
mtmorgan
closed
6 years ago
0
return vector from seqAlleleCount?
#23
smgogarten
closed
7 years ago
0
seqGDS2VCF creates an inverted GT on the VCF file
#22
AAvalos82
closed
7 years ago
1
possible bug in seqGetData(x, "$dosage")
#21
smgogarten
closed
7 years ago
0
"push+intersect" does not behave as expected
#20
smgogarten
closed
7 years ago
3
Alternate solution for removing VariantAnnotation dependency
#19
smgogarten
closed
7 years ago
0
Segfault with seqVCF2GDS
#18
cheesemania
closed
8 years ago
8
optimization
#17
zhengxwen
closed
8 years ago
0
added sample.annotation to colData
#16
smgogarten
closed
8 years ago
0
seqSlidingWindow exported?
#15
sa-lee
closed
8 years ago
3
use lengths instead of elementNROWS
#14
smgogarten
closed
8 years ago
0
bug fixes / updates to asVCF
#13
smgogarten
closed
8 years ago
0
bug fix in asVCF
#12
smgogarten
closed
8 years ago
0
a bug in seqParallel() (SeqArray_1.10.5)
#11
zhengxwen
closed
9 years ago
0
export methods for compatibility with VariantAnnotation
#10
smgogarten
closed
9 years ago
0
Is seqAlleleCount exported?
#9
DavisBrian
closed
9 years ago
2
function request: seqBED2GDS
#8
smgogarten
closed
9 years ago
0
duplicated "variant.id" when multiple VCF files were imported by seqVCF2GDS
#7
zhengxwen
closed
9 years ago
0
Generate GDS from VCF error
#6
cinaljess
closed
9 years ago
1
replace rowData with rowRanges
#5
smgogarten
closed
9 years ago
2
error while loading vcf file
#4
chisqr
closed
9 years ago
7
'by.sample' in seqApply
#3
zhengxwen
closed
9 years ago
0
fixed unit test related to VariantAnnotation update
#2
smgogarten
closed
10 years ago
0
Error in haploid genotypes (Y chromosome)
#1
zhengxwen
closed
10 years ago
1
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