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DecodeGenetics
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graphtyper
Population-scale genotyping using pangenome graphs
http://dx.doi.org/10.1038/ng.3964
MIT License
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better explanation of graphtyper output VCF
#104
edg1983
opened
2 years ago
2
<DEL:SVSIZE=0+:AGGREGATED>
#103
anxuan-web
opened
2 years ago
2
End - Start != SV size
#102
whtop
opened
2 years ago
0
Segmentation fault Reads with name=xxx both have IS_FIRST_IN_PAIR=1
#101
jjfarrell
opened
2 years ago
2
Can I use Graphtyper to genotype cattle samples?
#100
harbi811
closed
2 years ago
1
Genotyping SVs from other callers
#99
dr-ashu-geno
opened
2 years ago
3
Version 2.7.4
#98
hannespetur
closed
2 years ago
0
Adds binned PL scores
#97
hannespetur
closed
2 years ago
0
out-of-source builds and CMake clean-up
#96
h-2
closed
2 years ago
0
Update catch
#95
h-2
closed
2 years ago
2
Version 2.7.3
#94
hannespetur
closed
2 years ago
0
Not all variants with aggregated tag and many variants with low quality genotype
#93
biozzq
opened
2 years ago
1
FILTER!=PASS but FT=PASS
#92
biozzq
opened
2 years ago
0
Graphtyper outputs new alleles that are not in input VCF
#91
ivargr
opened
2 years ago
0
Filtering graphtyper output results in losing 98% of SVs
#90
dr-ashu-geno
closed
2 years ago
4
No OLD_VARIANT_ID?
#89
kmegq
opened
3 years ago
1
Binary of graphtyper runs extremely slow
#88
shangshanzhizhe
closed
3 years ago
4
Can graphtyper be used to genotype cancer samples ?
#87
rbr7
opened
3 years ago
1
SNV discovery from PacBio or Nanopore data
#86
twesigomwedavid
opened
3 years ago
4
Improves changes made in PR #82
#85
hannespetur
closed
3 years ago
0
Re-structuring of CMakeLists
#84
h-2
closed
2 years ago
3
Minor tweaks for HLA
#83
hannespetur
closed
3 years ago
0
Caller hap reworked
#82
hannespetur
closed
3 years ago
0
Version 2.7.2
#81
hannespetur
closed
3 years ago
2
HLA most common 4digit alleles
#80
hannespetur
closed
3 years ago
0
Add Clang tidy config
#79
hannespetur
closed
3 years ago
0
Fix IUPAC bug
#78
hannespetur
closed
3 years ago
0
Long read mapq adjustment
#77
hannespetur
closed
3 years ago
1
Replace the last of boost
#76
h-2
closed
3 years ago
0
Replace boost things
#75
h-2
closed
3 years ago
2
Clang format all the things
#74
hannespetur
closed
3 years ago
4
genotype_sv: can CRAMs be processed one-at-a-time?
#73
23andme-jaredo
closed
3 years ago
2
How to best filter duplicate calls in the output VCF to get one call per variant?
#72
jmonlong
opened
3 years ago
6
Long-read assemblies
#71
z1242099843
opened
3 years ago
6
Filtering SVs after genotyping by Graphtyper2
#70
Saeideh-Ashouri
closed
3 years ago
2
Genotyping both Indels and SVs
#69
jjfarrell
closed
3 years ago
2
Error in genotype reading temporary input fasta
#68
alexweisberg
opened
3 years ago
4
regenotyped samples produces all Genptype (GT) with ./.
#67
Solyris83
opened
3 years ago
8
Genotyping SNPs that are non-variable within dataset
#66
malmarri
closed
3 years ago
6
Minimum read length needed for genotype_sv?
#65
martinghunt
opened
3 years ago
5
FILTER=PASS but FT=FAIL1
#64
jjfarrell
opened
3 years ago
3
Using a SV vcf from other callers than Manta
#63
clairemerot
opened
3 years ago
4
Hello, I don't think it should need that much, less than 4GB per thread should be enough for 350 samples (assuming 30x coverage).
#62
koujiaodahan
closed
4 years ago
1
Applying variants with symbolic alleles made by genotype_sv
#61
bricoletc
closed
4 years ago
5
graphtyper genotyper_sv :<error> No regions specified
#60
y1025i
opened
4 years ago
3
Variant INFO/END position is before POS
#59
seboyden
opened
4 years ago
3
core dumped
#58
koujiaodahan
opened
4 years ago
13
genotype_sv [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/6aef897c3d6ff0c78aff06ac189178dd": Protocol not supported
#57
koujiaodahan
closed
3 years ago
2
How do I connect the input and output of the three software (manta+svimmer+graphtyper)
#56
koujiaodahan
opened
4 years ago
1
Fatal error "FAI index has no entry" for GRCh38 HLA alt contig
#55
seboyden
opened
4 years ago
6
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