hall-lab svtyper issues

hall-lab / svtyper

Bayesian genotyper for structural variants

MIT License

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issues

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Svtyper does not support TRA type.

#128 pingxinxing opened 5 months ago
0
Warning: Unsupported SVTYPE at variant MantaBND:93:0:1:0:1:0:0 (TRA). Skipping.

#127 pingxinxing opened 5 months ago
1
KeyError: 'RG'

#126 karen916 opened 1 year ago
0
how to filter SV using the "QUAL" threshold

#125 jackzhong1995 opened 1 year ago
0
Reference calls with no support and missing calls

#124 aariani opened 3 years ago
0
I have question about Genotype information in SVtyper output

#123 u1200538 opened 3 years ago
0
Issue while running the executable.

#122 kghimire09 opened 3 years ago
5
SVtyper on lumpy traditional vcf

#121 nitinra closed 3 years ago
1
update for original paper link

#120 esolares opened 4 years ago
0
Error during setup

#119 rsolano1-uw closed 4 years ago
2
Error: invalid FORMAT field, "+"

#118 edgarsierraorozco opened 4 years ago
0
The meaning of the parameters

#117 tyyiyi opened 4 years ago
0
Precise breakpoints

#116 biozzq opened 4 years ago
0
Failed to build insert size histogram for paired-end reads.

#115 tirohia opened 4 years ago
0
Key Error(s) being thrown for various call sets in C elegans

#114 moldach opened 4 years ago
0
annotate translocations with svtyper

#113 jazberna1 opened 4 years ago
2
Update svtyper to count reads at breakpoints separately

#112 anju24 closed 4 years ago
1
Fixed #103 (KeyError: 'CIPOS')

#111 mchowdh200 opened 4 years ago
6
update for python 3

#110 brentp opened 5 years ago
0
recommendation for numpy version for svtyper 0.7.1

#109 kgaonkar6 opened 5 years ago
0
How to understand the output genotyped from svtyper?

#108 xujinshengjsxu opened 5 years ago
0
Get the last > char

#107 apregier closed 5 years ago
0
is there a clear pipline for paired or tumor-only and json file is what? thanks a lot

#106 wentgithub opened 5 years ago
0
header parsing can't handle ">" in description

#105 brentp opened 5 years ago
3
svtyper-sso can not deal with multiple bam files?

#104 verne91 opened 5 years ago
0
KeyError: 'CIPOS'

#103 verne91 opened 5 years ago
1
How to merge the vcfs from different samples?

#102 verne91 closed 5 years ago
1
On making precision-recall curves: quality info? lenient parameters?

#101 jmonlong opened 5 years ago
0
Does svtyper calculate read pairs which have long overlap twice?

#100 xyw1 opened 5 years ago
0
SVtyper questions / issues

#99 calhoujd opened 5 years ago
0
Question about parameter 'max_reads' of classic svtyper.

#98 lss1227 opened 6 years ago
0
v0.7.0

#97 ernfrid closed 6 years ago
0
improve svtyper speed by ~30%

#96 brentp closed 6 years ago
3
Best FORMAT field for filtering SVTyper Output

#95 andrewSharo opened 6 years ago
2
SVtyper for SNVs/indels

#94 fpbarthel closed 6 years ago
2
Create svtyper-parallel

#93 dvanderleest opened 6 years ago
0
Multi core functionality missing for multisample projects

#92 dvanderleest closed 6 years ago
3
Lack of support for (b)gzipped vcf files and analysing only part(s) of the files (region support)

#91 dvanderleest opened 6 years ago
4
Question about DP

#90 panzhaodong123 opened 6 years ago
1
What's the meaning of QUAL = 0? is there an option to add -q to the Speedseq SV pipeline?

#89 Sithara85 opened 6 years ago
2
bamfile without index

#88 btoe opened 6 years ago
3
Can I use svtyper to genotype Hydra output?

#87 jiangyuanluo closed 6 years ago
1
svtyper on tumor/normal pair, which BAM to supply

#86 fpbarthel closed 6 years ago
3
Running SVTyper on any SV tool

#85 mej54 opened 6 years ago
8
output AD for depth

#84 brentp opened 6 years ago
0
Port code to python3 and add parallelization per individual

#83 florealcab opened 6 years ago
0
Stub in code for toggling use of 95 pct confidence interval

#82 ernfrid closed 6 years ago
1
problem in running svtyper

#81 ytguojian closed 6 years ago
4
if CI is too big, use CI95

#80 brentp closed 6 years ago
12
Fix bnd warning conditional

#79 ernfrid closed 6 years ago
0