Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / hall-lab/svtools issues and pull requests

#332 - GT:CN ./.:309.986

Issue - State: open - Opened by pingxinxing 4 months ago

#330 - vcftobedpe does not give strandedness for MANTA Outputs

Issue - State: open - Opened by think-o 6 months ago - 1 comment

#328 - svtools lsort KeyError: 'CIPOS'

Issue - State: open - Opened by hcsun1 8 months ago

#326 - svtools afreq KeyError: 'SQ' in

Issue - State: open - Opened by shameem356 over 1 year ago

#325 - ValueError: max() arg is an empty sequence

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

#324 - bedpetovcf does not work with vcftobedpe output as input

Issue - State: open - Opened by anoronh4 over 2 years ago - 1 comment

#322 - Not able to convert vcf to bedpe (Manta output)

Issue - State: open - Opened by Giuseppe1995 over 2 years ago

#321 - sv_classifier.py crash at calc_params if no del in training data.

Pull Request - State: open - Opened by jasonbhn over 2 years ago

#319 - Resolve incompatible Python dependencies

Pull Request - State: open - Opened by iainrb over 2 years ago

#318 - possible bug in TRA conversion

Issue - State: open - Opened by anoronh4 almost 3 years ago

#317 - Are lmerge same as l_merge.py scripts included in LUMPY?

Issue - State: open - Opened by sulinq about 3 years ago

#316 - lsort Index error

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

#315 - lmerge divide zero error

Issue - State: open - Opened by genostack about 3 years ago - 2 comments

#312 - pip install fails

Issue - State: open - Opened by anoronh4 over 3 years ago - 2 comments

#311 - Update vcftobedpe to support Delly 0.7.8 ouputs

Pull Request - State: open - Opened by whelena over 3 years ago

#310 - svtools vcfpaste error

Issue - State: open - Opened by KrithikaSubramanian over 3 years ago - 2 comments

#309 - No module named 'l_bp'

Issue - State: open - Opened by Avramis over 3 years ago - 1 comment

#308 - Python 3.6

Issue - State: open - Opened by mike-molnar almost 4 years ago

#307 - vcftobedpe complains about no END field in LUMPY BNDs.

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

#306 - Genotyping skips insertions (INS)

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

#305 - Does svtools support to mapping BEDPE to human genes?

Issue - State: open - Opened by Shicheng-Guo about 4 years ago

#304 - Syntax error msg

Issue - State: open - Opened by nitha26 about 4 years ago

#302 - Installation fails due to conflicting pandas version

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

#301 - vcftobedpe's output has one-based START coordinates instead of one-based

Issue - State: open - Opened by ManavalanG over 4 years ago - 1 comment

#300 - Installation error with Pip because some packages rely on Python3

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

#299 - merge error

Issue - State: open - Opened by lee039 almost 5 years ago - 2 comments

#298 - Svtools classify BNDing most of the DELs

Issue - State: open - Opened by brittanyhowell almost 5 years ago - 1 comment

#297 - svtools lsort

Issue - State: closed - Opened by marquispa almost 5 years ago - 2 comments

#296 - bedpetovcf crashes

Issue - State: open - Opened by johnemajor almost 5 years ago - 1 comment

#295 - prune's RETAINED criteria

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

#294 - Svtools classify raising ValueError exception

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

#292 - updates for python3

Pull Request - State: open - Opened by brentp about 5 years ago

#291 - Running SV-tools across combined VCFs with multiple SV call types

Issue - State: closed - Opened by oalavijeh about 5 years ago - 1 comment

#290 - Conda packaging no longer maintained

Pull Request - State: closed - Opened by apregier about 5 years ago - 1 comment

#289 - Changes for release

Pull Request - State: closed - Opened by apregier about 5 years ago - 1 comment

#288 - Clarification on classifier use and output

Issue - State: open - Opened by edg1983 over 5 years ago

#287 - Svtools copynumber error

Issue - State: open - Opened by deepalivasoya over 5 years ago - 1 comment

#286 - Updates for release

Pull Request - State: closed - Opened by apregier over 5 years ago - 1 comment

#285 - build high confidence call set for training

Issue - State: closed - Opened by edg1983 over 5 years ago

#284 - lsort sorting?

Issue - State: closed - Opened by jjfarrell over 5 years ago - 2 comments

#283 - create_coordinates: accept bgzipped VCF as input

Pull Request - State: closed - Opened by dantaki over 5 years ago - 1 comment

#282 - Mantamerging

Pull Request - State: closed - Opened by apregier over 5 years ago - 1 comment

#281 - vcftobedpe fails for certain MANTA calls

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

#280 - Difference between lmerge and prune?

Issue - State: open - Opened by gwct over 5 years ago - 2 comments

#279 - how to run svtools

Issue - State: open - Opened by Jordi-V almost 6 years ago

#278 - flip pos, END where needed

Pull Request - State: closed - Opened by brentp almost 6 years ago - 8 comments

#277 - Genotypes all converted to ./.

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

#276 - Not clear with the command to run svtools

Issue - State: closed - Opened by amrita1983 almost 6 years ago - 2 comments

#274 - lsort doest not merge multisamples run by lumpy

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

#273 - IndexError: list index out of range svtools copynumber

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

#272 - Pull in changes for svtools 0.4.0

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

#271 - Update to using svtyper 0.7.0

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

#270 - Joint genotyping multi-sample vcf

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

#269 - Initial draft of information on tiered merging

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

#268 - Svtyper and svtools genotype

Issue - State: closed - Opened by panzhaodong123 over 6 years ago - 3 comments

#267 - switch to ALG=SUM too eager?

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

#265 - Use whole chromosome to get CN

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

#256 - IndexError: list index out of range while running lsort

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

#255 - svtools lmerge error

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

#254 - Reintroduce test version of genotype refinement

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

#250 - Cannot update a set while iterating over it

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

#247 - KeyError: PE (lmerge step)

Issue - State: closed - Opened by MehmetGoktay almost 7 years ago - 15 comments

#238 - Chromosome parsing

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

#237 - the pre-result of CNVnator for svtools copynumber

Issue - State: closed - Opened by GangLiTarheel almost 7 years ago - 6 comments

#236 - Lsort ValueError: too many values to unpack

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

#235 - Set entire sample to missing CN if cnvnator fails

Pull Request - State: closed - Opened by ernfrid almost 7 years ago - 3 comments

#231 - Lsort File error handling

Issue - State: closed - Opened by ernfrid about 7 years ago - 1 comment

#230 - Breakpoint cleanup

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

#229 - Ensure we can reconstruct a Manta bedpe

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

#227 - Better handling of cnvnator copynumber value of -1

Issue - State: closed - Opened by ernfrid about 7 years ago - 8 comments

#226 - prune can occasionally yield a duplicate variant in the output

Issue - State: closed - Opened by ernfrid about 7 years ago - 1 comment
Labels: bug

#219 - Update documentation on sorting tools. Closes #183.

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

#218 - Support Manta VCFs for conversion to BEDPE

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

#217 - Add in a SUPPORT.md file

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

#215 - Mei documentation for GRCh38

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

#212 - Varlookup 209

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

#203 - lmerge/ prune workflow still results in overlapping calls

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

#202 - Add support for 8-column VCF input in lsort

Issue - State: closed - Opened by ernfrid over 7 years ago

#199 - work-flow

Issue - State: closed - Opened by brentp over 7 years ago - 6 comments

#197 - Warning: missing secondary multiline variant

Issue - State: closed - Opened by chrisamiller over 7 years ago - 3 comments

#195 - error out if there are duplicate samples in VCFs

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

#193 - IndexError: list index out of range

Issue - State: closed - Opened by atasub over 7 years ago - 1 comment
Labels: bug

#191 - Update svtyper0.1.2

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

#190 - script to compare overlaps by SNAME field

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

#180 - add a flag to identify variants that survived pruning of a cluster. This

Pull Request - State: closed - Opened by ernfrid about 8 years ago - 2 comments

#179 - Lsort improvements

Pull Request - State: closed - Opened by ernfrid about 8 years ago - 5 comments

#178 - Copynumber value handling

Pull Request - State: closed - Opened by ernfrid about 8 years ago - 2 comments

#177 - Fix pipe handling

Pull Request - State: closed - Opened by ernfrid about 8 years ago - 2 comments