DecodeGenetics graphtyper issues

DecodeGenetics / graphtyper

Population-scale genotyping using pangenome graphs

http://dx.doi.org/10.1038/ng.3964

MIT License

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issues

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Not able to handle missing sites

#154 Hjorvik opened 2 months ago
0
During installation, an error occurred: "c++: error: unrecognized command line option ‘-mavx512bw’"

#153 kuangzhuoran closed 2 months ago
1
Genotype_sv Aggregate model has less Output SVs than Input SVs

#152 Lukecassar21 opened 2 months ago
0
HLA-Genotyping: <error> Converting "HLA-A*01:01:01:01" of size 17 to int failed

#151 Lukecassar21 opened 4 months ago
3
Created chopped CRAI

#150 nathanLauHKGI opened 4 months ago
2
( AC / NUM_MERGED_SVS ) < 25

#149 weizhu365 opened 6 months ago
1
vcf_merge for SV

#148 JoannaTan opened 6 months ago
1
Is it possible to call STRs with graphtyper?

#147 scienception opened 6 months ago
1
In the genotype_sv result, the `REF` filed is N, and the `ALT` filed is not a sequence.

#146 tanger-code opened 8 months ago
0
Graphtyper for calling human X-chromosome variants

#145 Sirtx opened 8 months ago
0
REF in VCF file is N

#144 pingxinxing opened 10 months ago
0
Coordinates must be > 0

#143 carolinapinapaez opened 10 months ago
1
Genotype outputs all sites

#142 lihaicheng7003 opened 10 months ago
4
genotype wrong

#141 lihaicheng7003 opened 10 months ago
4
killed by the cgroup out-of-memory handler

#140 zhachengwan opened 11 months ago
1
why SVSIZE=number+

#139 jingydz opened 11 months ago
2
[WIP] Fix htslib configure issue

#138 hannespetur closed 11 months ago
0
Reads with name=dG both have IS_FIRST_IN_PAIR=0

#137 tanger-code closed 11 months ago
1
sample order in the output VCFs

#136 lindenb closed 11 months ago
2
genotyping small variant error, result only contains vcf header!

#135 tanger-code closed 11 months ago
3
Should there be no commas in the subsequent processing of the graphtyper output file that describes the document?

#134 jingydz closed 1 year ago
1
Not all Svimmer INS/DEL/DUP are genotyped by grapthyper as expected

#133 jjfarrell opened 1 year ago
2
Failing to produce calls for same samples

#132 buchanri opened 1 year ago
0
segment fault when genotyping sv

#131 dodudoduding opened 1 year ago
0
segment fault when genotyping sv

#130 dodudoduding opened 1 year ago
0
Genotyping of variants resulted from multi-sample Mutect2 (question)

#129 mkyriak opened 1 year ago
0
Graphtyper may introduce overlapped SVs in one individual

#128 jxcao98 opened 1 year ago
0
All BNDs have no FORMAT:FT

#127 tgong1 opened 1 year ago
6
Compiling graphtyper. Problem with include(`-I`) paths when compiling. /usr/include is ignored.

#126 lindenb opened 1 year ago
1
A few errors in my bams raise a std::exit(1);, how can I modify the C++ code to skip the read(s) ?

#125 lindenb closed 1 year ago
2
All chromosomes except chromosome 1 are LowPratio on the AGGREGATED model for DEL

#124 YiBenqiu opened 1 year ago
0
use clang++ make, fatal error: redefinition of 'this_compile_arch'

#123 liuyong201811 opened 1 year ago
1
LargeSVsize Filter; PASS?

#122 mplanasfelix opened 1 year ago
0
Call SVs by genome assemblies, and genotyped in WGS population

#121 QianghuiZhu opened 1 year ago
0
Use latest Paw from https://github.com/hannespetur/paw.git dev branch

#120 martin-g closed 1 year ago
2
When make, the following error occurs with the clang compiler on the ARM platform

#119 123xyl closed 1 year ago
1
vcf_operations.cpp:525 Sample names are not unique

#118 xuefenfei712 opened 1 year ago
1
arm64 installtion

#117 xiaopangjun666 closed 1 year ago
2
SV in input VCF missed in graphtyper output VCF

#116 tgong1 opened 1 year ago
2
problem about source code

#115 HuangseYuanli opened 1 year ago
1
Add support for Linux ARM64

#114 martin-g closed 1 year ago
3
INFO/AAScore using graphtyper 2.7.4 is missing

#113 jjfarrell closed 1 year ago
1
how to gain the sequence information

#112 zhoudreames closed 1 year ago
1
call and genotype Sv with population

#111 zhoudreames closed 1 year ago
1
[Question] Is ARM64 a supported architecture?

#110 markjens closed 1 year ago
6
I do not know how to add an insertion at position

#109 zongzone opened 2 years ago
2
COVERAGE model missing for DEL causing AGGREGATED model to fail

#108 Lee-06 opened 2 years ago
2
The genome size is too large to genotype for some genomic region properly !!!

#107 yinmou21 opened 2 years ago
1
What does that mean？（FT=FAIL1/FAIL2/FAIL3！）

#106 yinmou21 opened 2 years ago
2
HLA Typing

#105 malmarri closed 2 years ago
2