hall-lab/svtyper issues and pull requests

#128 - Svtyper does not support TRA type.

Issue - State: open - Opened by pingxinxing 8 months ago

#127 - Warning: Unsupported SVTYPE at variant MantaBND:93:0:1:0:1:0:0 (TRA). Skipping.

Issue - State: open - Opened by pingxinxing 9 months ago - 1 comment

#126 - KeyError: 'RG'

Issue - State: open - Opened by karen916 over 1 year ago

#125 - how to filter SV using the "QUAL" threshold

Issue - State: open - Opened by jackzhong1995 over 1 year ago

#124 - Reference calls with no support and missing calls

Issue - State: open - Opened by aariani over 3 years ago

#123 - I have question about Genotype information in SVtyper output

Issue - State: open - Opened by omG0-hub over 3 years ago

#122 - Issue while running the executable.

Issue - State: open - Opened by kghimire09 almost 4 years ago - 5 comments

#121 - SVtyper on lumpy traditional vcf

Issue - State: closed - Opened by nitinra about 4 years ago - 1 comment

#120 - update for original paper link

Issue - State: open - Opened by esolares over 4 years ago

#119 - Error during setup

Issue - State: closed - Opened by rsolano1-uw over 4 years ago - 2 comments

#118 - Error: invalid FORMAT field, "+"

Issue - State: open - Opened by edgarsierraorozco over 4 years ago

#117 - The meaning of the parameters

Issue - State: open - Opened by tyyiyi over 4 years ago

#116 - Precise breakpoints

Issue - State: open - Opened by biozzq over 4 years ago

#115 - Failed to build insert size histogram for paired-end reads.

Issue - State: open - Opened by tirohia over 4 years ago

#114 - Key Error(s) being thrown for various call sets in C elegans

Issue - State: open - Opened by moldach almost 5 years ago

#113 - annotate translocations with svtyper

Issue - State: open - Opened by jazberna1 almost 5 years ago - 2 comments

#112 - Update svtyper to count reads at breakpoints separately

Pull Request - State: closed - Opened by anju24 almost 5 years ago - 1 comment

#111 - Fixed #103 (KeyError: 'CIPOS')

Pull Request - State: open - Opened by mchowdh200 about 5 years ago - 6 comments

#110 - update for python 3

Pull Request - State: open - Opened by brentp over 5 years ago - 1 comment

#109 - recommendation for numpy version for svtyper 0.7.1

Issue - State: open - Opened by kgaonkar6 over 5 years ago

#108 - How to understand the output genotyped from svtyper?

Issue - State: open - Opened by xujinshengjsxu over 5 years ago

#107 - Get the last > char

Pull Request - State: closed - Opened by apregier over 5 years ago

#106 - is there a clear pipline for paired or tumor-only and json file is what? thanks a lot

Issue - State: open - Opened by wentgithub over 5 years ago

#105 - header parsing can't handle ">" in description

Issue - State: open - Opened by brentp over 5 years ago - 3 comments

#104 - svtyper-sso can not deal with multiple bam files?

Issue - State: open - Opened by verne91 almost 6 years ago

#103 - KeyError: 'CIPOS'

Issue - State: open - Opened by verne91 almost 6 years ago - 1 comment

#102 - How to merge the vcfs from different samples?

Issue - State: closed - Opened by verne91 almost 6 years ago - 1 comment

#101 - On making precision-recall curves: quality info? lenient parameters?

Issue - State: open - Opened by jmonlong almost 6 years ago

#100 - Does svtyper calculate read pairs which have long overlap twice?

Issue - State: open - Opened by xyw1 about 6 years ago

#99 - SVtyper questions / issues

Issue - State: open - Opened by calhoujd about 6 years ago

#98 - Question about parameter 'max_reads' of classic svtyper.

Issue - State: open - Opened by lss1227 over 6 years ago

#97 - v0.7.0

Pull Request - State: closed - Opened by ernfrid over 6 years ago

#96 - improve svtyper speed by ~30%

Pull Request - State: closed - Opened by brentp over 6 years ago - 3 comments

#95 - Best FORMAT field for filtering SVTyper Output

Issue - State: open - Opened by andrewSharo over 6 years ago - 2 comments

#94 - SVtyper for SNVs/indels

Issue - State: closed - Opened by fpbarthel over 6 years ago - 2 comments

#93 - Create svtyper-parallel

Pull Request - State: open - Opened by ikkextoch over 6 years ago

#92 - Multi core functionality missing for multisample projects

Issue - State: closed - Opened by ikkextoch over 6 years ago - 3 comments

#91 - Lack of support for (b)gzipped vcf files and analysing only part(s) of the files (region support)

Issue - State: open - Opened by ikkextoch over 6 years ago - 4 comments

#90 - Question about DP

Issue - State: open - Opened by panzhaodong123 over 6 years ago - 1 comment

#89 - What's the meaning of QUAL = 0? is there an option to add -q to the Speedseq SV pipeline?

Issue - State: open - Opened by Sithara85 over 6 years ago - 2 comments

#88 - bamfile without index

Issue - State: open - Opened by btoe over 6 years ago - 3 comments

#87 - Can I use svtyper to genotype Hydra output?

Issue - State: closed - Opened by jiangyuanluo over 6 years ago - 1 comment

#86 - svtyper on tumor/normal pair, which BAM to supply

Issue - State: closed - Opened by fpbarthel over 6 years ago - 3 comments

#85 - Running SVTyper on any SV tool

Issue - State: open - Opened by mej54 over 6 years ago - 8 comments

#84 - output AD for depth

Issue - State: open - Opened by brentp over 6 years ago

#83 - Port code to python3 and add parallelization per individual

Pull Request - State: open - Opened by florealcab almost 7 years ago

#82 - Stub in code for toggling use of 95 pct confidence interval

Pull Request - State: closed - Opened by ernfrid almost 7 years ago - 1 comment

#81 - problem in running svtyper

Issue - State: closed - Opened by ytguojian almost 7 years ago - 4 comments

#80 - if CI is too big, use CI95

Pull Request - State: closed - Opened by brentp almost 7 years ago - 12 comments

#79 - Fix bnd warning conditional

Pull Request - State: closed - Opened by ernfrid almost 7 years ago

#78 - set alt clip to 0 if there is no other alt support

Pull Request - State: closed - Opened by brentp almost 7 years ago - 5 comments

#77 - error/warning on singleton BND

Issue - State: closed - Opened by brentp almost 7 years ago - 1 comment

#76 - Turn off library messages by default

Pull Request - State: closed - Opened by ernfrid about 7 years ago - 2 comments

#75 - svtyper-classic: only print Reading metrics message once

Pull Request - State: closed - Opened by brentp about 7 years ago - 2 comments

#74 - python3 svtyper

Issue - State: open - Opened by thomasfaraut about 7 years ago - 3 comments

#73 - Genotyping calculation improvements

Pull Request - State: closed - Opened by ernfrid about 7 years ago

#72 - Update pysam dependency to pysam>=0.12.0

Pull Request - State: closed - Opened by ernfrid about 7 years ago

#71 - Using svtyper for other sv callers

Issue - State: open - Opened by MehmetGoktay about 7 years ago - 3 comments

#70 - argument list too long

Issue - State: closed - Opened by GangLiTarheel about 7 years ago

#69 - speed up options

Issue - State: open - Opened by ramaniak about 7 years ago - 2 comments

#68 - SVtyper: Filtering Svs based on qual Column

Issue - State: open - Opened by MehmetGoktay about 7 years ago

#67 - organizational revamp and multicore feature

Pull Request - State: closed - Opened by indraniel over 7 years ago - 2 comments

#66 - recommendations for pysam version

Issue - State: closed - Opened by Kurt-Hetrick over 7 years ago - 2 comments

#65 - Reference genotypes with no support

Issue - State: open - Opened by ernfrid over 7 years ago - 1 comment

#64 - KeyError: 'MATEID'

Issue - State: open - Opened by YiweiNiu over 7 years ago - 3 comments

#63 - SVTyper discarding VCF entries

Issue - State: open - Opened by CBorreda over 7 years ago

#62 - How to genotype many samples

Issue - State: open - Opened by 54tuifeimo over 7 years ago - 1 comment

#61 - Update README.md to correctly clone repo

Pull Request - State: closed - Opened by avakel over 7 years ago - 1 comment

#60 - Question

Issue - State: open - Opened by ldorozco over 7 years ago - 2 comments

#59 - Error while processing Lumpy results

Issue - State: open - Opened by arp31089 over 7 years ago - 3 comments

#58 - memory error

Issue - State: open - Opened by djakubosky almost 8 years ago - 2 comments

#57 - dont grab lib (and read group) unless needed and no copy

Pull Request - State: closed - Opened by brentp almost 8 years ago

#56 - limit number of reads in gather_reads

Pull Request - State: closed - Opened by brentp almost 8 years ago

#55 - unknown error <- the worst bug report.

Issue - State: closed - Opened by zeeev almost 8 years ago - 2 comments

#54 - Improve breakpoint support evaluation

Pull Request - State: closed - Opened by ernfrid about 8 years ago

#53 - Update labeling of soft-clip support

Pull Request - State: closed - Opened by ernfrid over 8 years ago - 1 comment

#52 - add in separate tracking of clipped read support of alts.

Pull Request - State: closed - Opened by ernfrid over 8 years ago

#51 - AttributeError: 'csamtools.AlignedRead' object has no attribute 'has_tag'

Issue - State: closed - Opened by aj03 over 8 years ago - 1 comment

#50 - svtyper stucks

Issue - State: closed - Opened by woodoo46 over 8 years ago - 2 comments

#49 - (WIP) Split order

Pull Request - State: closed - Opened by ernfrid over 8 years ago

#48 - added necessary vcf #38

Pull Request - State: closed - Opened by cc2qe over 8 years ago

#47 - update travis tests #38

Pull Request - State: closed - Opened by cc2qe over 8 years ago

#46 - (WIP) Fixes to splitread identification

Pull Request - State: closed - Opened by ernfrid over 8 years ago

#45 - Remove dead code block

Pull Request - State: closed - Opened by ernfrid over 8 years ago

#44 - V0.1.0 updates

Pull Request - State: closed - Opened by cc2qe over 8 years ago

#43 - V0.1.0 updates

Pull Request - State: closed - Opened by cc2qe over 8 years ago

#42 - v0.1.0 readme, help menu

Pull Request - State: closed - Opened by cc2qe over 8 years ago

#41 - v0.1.0 release candidate

Pull Request - State: closed - Opened by cc2qe over 8 years ago

#40 - updates to v0.1.0

Pull Request - State: closed - Opened by cc2qe over 8 years ago

#39 - SVTYPE=INS

Issue - State: closed - Opened by zeeev over 8 years ago - 2 comments

#38 - Update test for v0.1.0

Issue - State: closed - Opened by ernfrid over 8 years ago

#37 - AttributeError: 'pysam.csamtools.AlignedRead' object has no attribute 'inferred_length'

Issue - State: closed - Opened by bjkelly over 8 years ago - 3 comments

#36 - 'module' object has no attribute 'AlignmentFile'

Issue - State: closed - Opened by srynobio over 8 years ago - 5 comments

#35 - CRAM support

Issue - State: closed - Opened by cc2qe over 8 years ago
Labels: enhancement

#34 - more robust header parsing (#23)

Pull Request - State: closed - Opened by cc2qe over 8 years ago

#27 - reads dropped in non deletion events

Issue - State: closed - Opened by cc2qe almost 9 years ago - 1 comment

#24 - Dropping reference support in certain cases

Issue - State: open - Opened by mlinderm almost 9 years ago - 2 comments
Labels: enhancement

#23 - Something funny about reading header

Issue - State: closed - Opened by ryanlayer about 9 years ago - 1 comment

#17 - VCF header preservation

Issue - State: closed - Opened by cc2qe over 9 years ago - 1 comment
Labels: bug

#16 - Downsample high depth regions

Issue - State: closed - Opened by cc2qe over 9 years ago - 1 comment

GitHub / hall-lab/svtyper issues and pull requests