hall-lab/svtyper issues and pull requests

#126 - KeyError: 'RG'

Issue - State: open - Opened by karen916 9 months ago

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

Issue - State: open - Opened by jackzhong1995 12 months ago

#124 - Reference calls with no support and missing calls

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

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

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

#122 - Issue while running the executable.

Issue - State: open - Opened by kghimire09 about 3 years ago - 3 comments

#121 - SVtyper on lumpy traditional vcf

Issue - State: closed - Opened by nitinra over 3 years ago

#120 - update for original paper link

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

#119 - Error during setup

Issue - State: closed - Opened by rsolano1-uw almost 4 years ago - 1 comment

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

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

#117 - The meaning of the parameters

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

#116 - Precise breakpoints

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

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

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

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

Issue - State: open - Opened by moldach about 4 years ago

#113 - annotate translocations with svtyper

Issue - State: open - Opened by jazberna1 about 4 years ago - 1 comment

#112 - Update svtyper to count reads at breakpoints separately

Pull Request - State: closed - Opened by anju24 over 4 years ago - 1 comment

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

Pull Request - State: open - Opened by mchowdh200 over 4 years ago - 6 comments

#110 - update for python 3

Pull Request - State: open - Opened by brentp over 4 years ago

#109 - recommendation for numpy version for svtyper 0.7.1

Issue - State: open - Opened by kgaonkar6 over 4 years ago

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

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

#107 - Get the last > char

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

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

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

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

Issue - State: open - Opened by verne91 about 5 years ago

#103 - KeyError: 'CIPOS'

Issue - State: open - Opened by verne91 about 5 years ago - 1 comment

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

Issue - State: closed - Opened by verne91 over 5 years ago - 1 comment

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

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

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

Issue - State: open - Opened by xyw1 over 5 years ago

#99 - SVtyper questions / issues

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

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

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

#97 - v0.7.0

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

#96 - improve svtyper speed by ~30%

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

#95 - Best FORMAT field for filtering SVTyper Output

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

#94 - SVtyper for SNVs/indels

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

#93 - Create svtyper-parallel

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

#92 - Multi core functionality missing for multisample projects

Issue - State: closed - Opened by ikkextoch almost 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 almost 6 years ago - 4 comments

#90 - Question about DP

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

#88 - bamfile without index

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

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

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

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

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

#85 - Running SVTyper on any SV tool

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

#84 - output AD for depth

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

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

Pull Request - State: open - Opened by florealcab about 6 years ago

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

Pull Request - State: closed - Opened by ernfrid about 6 years ago - 1 comment

#81 - problem in running svtyper

Issue - State: closed - Opened by ytguojian about 6 years ago - 4 comments

#80 - if CI is too big, use CI95

Pull Request - State: closed - Opened by brentp over 6 years ago - 12 comments

#79 - Fix bnd warning conditional

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

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

Pull Request - State: closed - Opened by brentp over 6 years ago - 5 comments

#77 - error/warning on singleton BND

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

#76 - Turn off library messages by default

Pull Request - State: closed - Opened by ernfrid over 6 years ago - 2 comments

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

Pull Request - State: closed - Opened by brentp over 6 years ago - 2 comments

#74 - python3 svtyper

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

#73 - Genotyping calculation improvements

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

#72 - Update pysam dependency to pysam>=0.12.0

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

#71 - Using svtyper for other sv callers

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

#70 - argument list too long

Issue - State: closed - Opened by GangLiTarheel over 6 years ago

#69 - speed up options

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

#68 - SVtyper: Filtering Svs based on qual Column

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

#67 - organizational revamp and multicore feature

Pull Request - State: closed - Opened by indraniel over 6 years ago - 2 comments

#66 - recommendations for pysam version

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

#65 - Reference genotypes with no support

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

#64 - KeyError: 'MATEID'

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

#63 - SVTyper discarding VCF entries

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

#62 - How to genotype many samples

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

#61 - Update README.md to correctly clone repo

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

#60 - Question

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

#59 - Error while processing Lumpy results

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

#58 - memory error

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

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

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

#56 - limit number of reads in gather_reads

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

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

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

#54 - Improve breakpoint support evaluation

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

#53 - Update labeling of soft-clip support

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

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

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

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

Issue - State: closed - Opened by aj03 over 7 years ago - 1 comment

#50 - svtyper stucks

Issue - State: closed - Opened by woodoo46 over 7 years ago - 2 comments