Ecosyste.ms: Issues

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

GitHub / AstraZeneca-NGS/VarDictJava issues and pull requests

#397 - some variant can't output in two reapeat sample

Issue - State: open - Opened by litun-fkby about 1 year ago

#396 - Current and future support for Vardict

Issue - State: open - Opened by alexander-e-f-smith about 1 year ago - 2 comments

#395 - the option -3 result

Issue - State: open - Opened by litun-fkby over 1 year ago

#394 - question about ODDRATIO

Issue - State: open - Opened by litun-fkby over 1 year ago

#393 - Running error

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

#392 - SNP vs SNV

Issue - State: closed - Opened by LeilyR over 1 year ago

#391 - Can I get the read names of a variant?

Issue - State: open - Opened by Crispy13 over 1 year ago

#387 - The AF value VarDict calculate cannot match with IGV result.

Issue - State: open - Opened by GA-1101 almost 2 years ago

#386 - AF > 1 with DP < VD for some Long deletions

Issue - State: open - Opened by alexander-e-f-smith almost 2 years ago - 2 comments

#385 - Having trouble downloading Vardict 1.8.3 through wget

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

#384 - JAVA ERROR RUNNING VARDICTJAVA

Issue - State: open - Opened by espelpz almost 2 years ago - 3 comments

#383 - vardict can not call the mutation correctly

Issue - State: open - Opened by wyy1234-github almost 2 years ago

#382 - VCF merging between Mutect2 and VarDict output fail

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

#380 - cram input

Issue - State: open - Opened by GSBaohuaGu almost 2 years ago - 1 comment

#379 - cram

Issue - State: closed - Opened by GSBaohuaGu almost 2 years ago

#378 - Possible formatting issue in the somatic mode

Issue - State: open - Opened by amunzur almost 2 years ago

#377 - ADJAF - Adjusted AF for indels due to local realignment

Issue - State: open - Opened by lt11 about 2 years ago - 1 comment

#375 - ArrayIndexOutOfBoundsException

Issue - State: open - Opened by ds21uab about 2 years ago

#374 - UMI-based variant calling

Issue - State: open - Opened by andreakv93 about 2 years ago

#373 - Memory troubles

Issue - State: closed - Opened by lt11 about 2 years ago - 8 comments

#370 - WGS non-human data -- taking a long time to call a single chromosome

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

#369 - Variant reported out of region of interest

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

#367 - EGFR EXON19 frameshit

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

#366 - Allele frequency parameter in VarDictJava

Issue - State: closed - Opened by ds21uab over 2 years ago - 1 comment

#364 - Using CRAM files with VarDictJava

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

#363 - Deletion is being called as complex variant

Issue - State: open - Opened by lk9-lnx almost 3 years ago - 2 comments

#362 - Mutation detection failed

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

#361 - Is it possible to filter orientation bias?

Issue - State: closed - Opened by kimjr89 almost 3 years ago - 1 comment

#360 - call a vaiant without chr and position, just the following info

Issue - State: open - Opened by asmlgkj almost 3 years ago - 4 comments

#359 - No line found error in the java version, works in the perl version

Issue - State: closed - Opened by rglusic almost 3 years ago - 1 comment

#357 - Variant with quality only gets called when decreasing the minimum phred score

Issue - State: closed - Opened by rollf almost 3 years ago - 4 comments

#356 - variation different between Single Sample Mode and Single Sample Mode

Issue - State: open - Opened by wangxuedong930227 almost 3 years ago - 1 comment

#355 - Paired Variant Calling lost variation

Issue - State: closed - Opened by wangxuedong930227 almost 3 years ago

#354 - -th option

Issue - State: closed - Opened by lk9-lnx almost 3 years ago

#353 - Haploid mutations calling

Issue - State: open - Opened by liuzhen51032 almost 3 years ago

#352 - werid EGFR variant report

Issue - State: open - Opened by asmlgkj almost 3 years ago - 1 comment

#350 - Vardict 1.8.3 outputs 37 columns in simple mode

Issue - State: closed - Opened by tgeneste about 3 years ago - 6 comments

#349 - Variant not passing VarDict filters

Issue - State: closed - Opened by aldosr about 3 years ago - 2 comments

#348 - Problem upgrading from Perl Vardict to Java Vardict

Issue - State: open - Opened by Graeme-Smith about 3 years ago - 1 comment

#347 - Updated submodule and version for 1.8.3

Pull Request - State: closed - Opened by PolinaBevad over 3 years ago

#344 - GT vardict info

Issue - State: closed - Opened by asmlgkj over 3 years ago - 1 comment

#343 - z

Issue - State: closed - Opened by worker000000 over 3 years ago

#342 - <dup-10> in one of the alternate alleles

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

#341 - index out of bound error related to hard clipping STILL an issue

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

#340 - Last position of Complex variant shows as SNV

Issue - State: closed - Opened by arturotorreso over 3 years ago - 4 comments

#339 - AF vs HIAF

Issue - State: closed - Opened by jsha129 over 3 years ago - 2 comments

#338 - NumberFormatException

Issue - State: closed - Opened by marrip over 3 years ago - 1 comment

#337 - PMean value description requires a bit more extra explanation

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

#336 - Sterimol descriptors with a python chemistry lib like chemlib

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

#335 - Travis CI update (faster/optimization) exclusively made for AstraZeneca

Pull Request - State: open - Opened by Montana almost 4 years ago

#334 - Variants in amplicon samples

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

#333 - Not reporting the correct contig length

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

#332 - Adaptors in local realignment

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

#331 - My Travis CI Update for AstraZeneca optimization

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

#329 - Question about FILTER and AF threshold

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

#328 - -L option for <DUP> structural variants

Issue - State: open - Opened by NEOGrok almost 4 years ago - 2 comments

#326 - Duplication variant called with Strand Bias issue

Issue - State: open - Opened by alexander-e-f-smith almost 4 years ago

#325 - Variants missing in amplicon samples

Issue - State: open - Opened by PabloCabaleiro about 4 years ago - 2 comments

#324 - log/progress file

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

#323 - Sum of AD field not matching DP

Issue - State: open - Opened by elleira over 4 years ago - 5 comments

#322 - why can I use "qsub" to run the VarDict task?

Issue - State: closed - Opened by windtalker6 over 4 years ago - 2 comments

#321 - Missing genotype/format fields improperly formatted

Issue - State: closed - Opened by nh13 over 4 years ago - 1 comment

#319 - Version and integration tests for VCF 4.2

Pull Request - State: closed - Opened by PolinaBevad over 4 years ago

#318 - test and p-value for step iv of vardict workflow

Issue - State: closed - Opened by ALFLAG over 4 years ago - 3 comments

#317 - Integration tests updates

Pull Request - State: closed - Opened by PolinaBevad over 4 years ago

#316 - Depth != RefFwdReads + RefRevReads

Issue - State: open - Opened by gudeqing over 4 years ago - 3 comments

#315 - Meaning of -3 option

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

#314 - add conda and usegalaxy badge

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

#313 - Paired variant calling how to set the value of option "-k"

Issue - State: open - Opened by liuzhen51032 over 4 years ago - 1 comment

#312 - A germline SNV called as somatic

Issue - State: open - Opened by Gerde over 4 years ago - 2 comments

#311 - Bam file with realigned reads

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

#310 - Removed updated comment from release script

Pull Request - State: closed - Opened by PolinaBevad over 4 years ago

#309 - Q) --deldupvar option

Issue - State: closed - Opened by dauss75 over 4 years ago - 2 comments

#308 - Description of any thresholds/limits used in SV/DUP detection?

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

#307 - Added fixes to integration tests

Pull Request - State: closed - Opened by PolinaBevad over 4 years ago

#306 - insertion position and length seems to not right

Issue - State: open - Opened by shiwanyin over 4 years ago - 5 comments

#305 - Only one variant identified

Issue - State: closed - Opened by luisacusick over 4 years ago - 6 comments

#304 - running with -P 1 seems not to work well

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

#303 - Add support for single primer amplicon designs

Pull Request - State: closed - Opened by jhl667 over 4 years ago - 1 comment

#301 - Amplicon Mode for QIAseq Designs

Issue - State: open - Opened by jhl667 over 4 years ago - 6 comments

#300 - Running on WGS data

Issue - State: closed - Opened by vymao over 4 years ago - 8 comments

#299 - VCF records with missing REF field are output in gVCF

Issue - State: closed - Opened by mjhipp over 4 years ago - 5 comments

#297 - Fix for REF variants in amplicon pileup mode

Pull Request - State: closed - Opened by PolinaBevad over 4 years ago

#296 - PMean value is incorrectly or confusingly reported.

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

#294 - No locations given "REF" in amplicon mode with -p

Issue - State: closed - Opened by jasteen almost 5 years ago - 7 comments

#293 - Fix issue 283 hardclips Index out of range error

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