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STITCH
STITCH - Sequencing To Imputation Through Constructing Haplotypes
http://www.nature.com/ng/journal/v48/n8/abs/ng.3594.html
GNU General Public License v3.0
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error in priorSum_m[, s]: incorrect number of dimensions
#98
pdimens
opened
1 week ago
6
no vcf file provided - SNPs with called genotype are imputed
#97
SelinaKlees
opened
1 month ago
4
pet and keyboard accident, please delete
#96
kiran-lee
closed
2 months ago
0
Assessing imputation accuracy
#95
kiran-lee
opened
3 months ago
4
possible error in validating the genetic map
#94
Ahhgust
opened
4 months ago
1
Error with function load_rhb_at_positions_no_NAs
#93
jamonterotena
opened
5 months ago
4
Forced imputation of founders. Does it make sense?
#92
GoliczGenomeLab
closed
5 months ago
2
Error: Execution halted
#91
Janelle555
opened
7 months ago
4
Error in validate_posfile(posfile) : Cannot find supplied posfile:10
#90
wy-cmd
closed
7 months ago
0
Output for ancestral haplotype probabilities?
#89
jamonterotena
opened
7 months ago
16
Fatal error during STITCH installation related to zlib.h
#88
jamonterotena
opened
8 months ago
2
genfile meaning and r^2
#87
SelinaKlees
opened
8 months ago
1
stitch crashed
#86
rmott
opened
9 months ago
5
It seems a bug in the function "findRecombinedReadsPerSample" at file "heuristics.R"
#85
wykkyle
closed
10 months ago
2
STITCH crashed
#84
rmott
opened
11 months ago
11
Docker container
#83
saulpierotti
closed
10 months ago
1
Segmentation fault MRE
#82
saulpierotti
closed
1 year ago
4
Some curious observations on STITCH results
#81
saulpierotti
opened
1 year ago
4
Running from command line 'Execution halted'
#80
mnbrien
closed
1 year ago
2
A question about readChar
#79
Dengzhaoo
closed
1 year ago
9
A question about copying files onto tempdir
#78
Dengzhaoo
closed
1 year ago
9
question about CRAM input format
#77
2584589300
closed
1 year ago
0
Suppress (or redirect) terminal prompts
#76
pdimens
closed
1 year ago
1
A question about info score
#75
Antennaria
opened
1 year ago
1
Seqlib
#74
rwdavies
closed
1 year ago
0
Some questions about input file making
#73
RADIOMUMM
opened
1 year ago
5
Segfault
#72
saulpierotti
closed
1 year ago
8
Clarification in the usage of the parameter S
#71
ghost
closed
1 year ago
1
Memory not mapped Problem
#70
cron-weasley
closed
1 year ago
9
downsample sample error
#69
Deeeeen
closed
1 year ago
2
genfile sample names
#68
GuyReeves
opened
2 years ago
14
--genfile its value and generating the file
#67
GuyReeves
opened
2 years ago
3
--generateInputOnly adding a single bam file to an existing processed dataset
#66
GuyReeves
closed
2 years ago
2
Read Length Normalization
#65
Deeeeen
closed
2 years ago
2
nCore causes problem
#64
Deeeeen
closed
2 years ago
1
get_and_initialize_from_reference, sample_haps_to_use, Negative probability
#63
Deeeeen
closed
2 years ago
5
Samples with a large amount of missing sites after imputation
#62
GuyReeves
opened
2 years ago
11
Parameter Setting
#61
lile19920725
opened
2 years ago
1
Is there a way to avoid having to Load and convert BAMs..... each run
#60
GuyReeves
opened
2 years ago
8
K optimization: r2 vs score
#59
nbedelman
opened
2 years ago
2
Missing genotypes even after imputation
#58
EveTC
opened
2 years ago
7
Create plots from output
#57
nbedelman
closed
1 year ago
3
Error in check_mclapply_OK(single_iteration_results)
#56
Deeeeen
closed
2 years ago
1
How to run pseudo-haploid and haploid
#55
MartinGiap
opened
2 years ago
1
running program error
#54
yao-chenxin
opened
2 years ago
1
Hi, can you post an example of what your file currently gives you? I suspect you are getting phased output from tped, whereas gen.txt is not phased but the unphased genotype, so you would add together phased output in the obvious way to get unphased genotype. I can offer suggestions on this if you post part of an example. Note that gen.txt is optional, you don’t need it to run STITCH, it is just helpful to show accuracy as you progress through the EM algorithm
#53
yao-chenxin
closed
2 years ago
0
How to use stitch
#52
YQ511
closed
2 years ago
1
how to produce input file
#51
yao-chenxin
opened
2 years ago
1
Intermediate .RData files to outputs VCF format
#50
lanxianmei
closed
1 year ago
2
A question about the results of STITCH
#49
Tengjun0520
closed
1 year ago
4
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