Ecosyste.ms: Issues

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GitHub / dellytools/delly issues and pull requests

#364 - about somatic SV calling

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

#363 - somatic pre filtering issue

Issue - State: closed - Opened by NidhiAgrawal27 9 months ago - 2 comments

#362 - min and max SV size

Issue - State: closed - Opened by skeremaydin 9 months ago - 3 comments

#361 - merging vcfs of various SV types (delly or bcftools?)

Issue - State: closed - Opened by shaghayeghsoudi 9 months ago - 2 comments
Labels: question

#360 - Somatic CNA's with tumor purity

Issue - State: open - Opened by yashcrux 9 months ago - 3 comments
Labels: question

#359 - Question about Algorithm Updates in Delly V2

Issue - State: open - Opened by ipstone 10 months ago - 1 comment
Labels: question

#358 - Delly vcf output

Issue - State: open - Opened by Ana1335 10 months ago - 3 comments
Labels: question

#357 - END position changed between delly 1.1.6 and 1.1.7

Issue - State: closed - Opened by Stikus 10 months ago - 2 comments
Labels: question

#356 - Delly call output --only have one type of SV (Deletions)

Issue - State: closed - Opened by XIAO2Mark 12 months ago - 1 comment

#355 - Delly call on WGS data

Issue - State: closed - Opened by Ceonham 12 months ago - 3 comments
Labels: bug

#354 - Realignment and break points

Issue - State: open - Opened by mmnikolic about 1 year ago - 3 comments
Labels: question

#353 - call CNV using a PON

Issue - State: closed - Opened by lmanchon about 1 year ago - 1 comment

#352 - MAPQ quality threshold

Issue - State: closed - Opened by AriadnaColmeneroCobo about 1 year ago - 1 comment

#350 - One SV with two records

Issue - State: closed - Opened by jackzhong1995 about 1 year ago - 1 comment

#349 - Two INV just differ by only 1 base

Issue - State: closed - Opened by jackzhong1995 about 1 year ago - 4 comments

#347 - Why SRs are reported when no PEs are indicated

Issue - State: closed - Opened by AriadnaColmeneroCobo about 1 year ago - 1 comment

#346 - how to merge the SV into genome

Issue - State: closed - Opened by tinyfallen about 1 year ago - 3 comments

#345 - Delly call sv by ont long-reads

Issue - State: closed - Opened by jackzhong1995 about 1 year ago - 2 comments

#344 - About the INS sequence in vcf output

Issue - State: open - Opened by ClarenceHsiang about 1 year ago - 4 comments

#343 - About the output format

Issue - State: closed - Opened by ClarenceHsiang about 1 year ago - 2 comments

#342 - SVLEN missing in output / INSLEN in all output

Issue - State: open - Opened by NicolaLady about 1 year ago - 1 comment

#341 - SV calling

Issue - State: open - Opened by fangling0913 about 1 year ago

#340 - 1

Issue - State: closed - Opened by xxxww11 about 1 year ago

#339 - Excluded regions

Issue - State: open - Opened by bounlu about 1 year ago - 1 comment

#338 - `BAM` file type

Issue - State: closed - Opened by bounlu about 1 year ago - 3 comments

#337 - Delly on WGBS data

Issue - State: open - Opened by bounlu about 1 year ago - 1 comment

#336 - Creating a mappability map

Issue - State: open - Opened by Immortal2333 about 1 year ago - 1 comment

#335 - Creating a mappability map

Issue - State: closed - Opened by Immortal2333 about 1 year ago - 1 comment

#334 - Delly on WGBS / methylseq data

Issue - State: closed - Opened by bounlu about 1 year ago - 1 comment

#333 - calling results for SR and RR/RV

Issue - State: closed - Opened by asaki1986 about 1 year ago - 2 comments

#332 - BAM files have different number of chromosomes!

Issue - State: closed - Opened by nash5202 about 1 year ago - 2 comments

#331 - very quick runtime

Issue - State: closed - Opened by heidihyang about 1 year ago

#330 - apply delly on RNA sequencing data

Issue - State: closed - Opened by asaki1986 about 1 year ago - 1 comment

#329 - CNV segmentation issue

Issue - State: open - Opened by jiadong324 about 1 year ago - 3 comments
Labels: enhancement

#328 - split-read assembly fault (Segmentation fault (core dumped))

Issue - State: open - Opened by zhanghanqing1992 over 1 year ago - 4 comments

#327 - The index file is older than the data file

Issue - State: closed - Opened by mxiong2 over 1 year ago - 1 comment

#326 - delly_v1.1.6 cnv failed

Issue - State: open - Opened by lmanchon over 1 year ago - 1 comment

#325 - Mappability map for the latest human reference genome T2T-CHM13

Issue - State: open - Opened by zacshi over 1 year ago - 5 comments
Labels: enhancement

#323 - Files for input

Issue - State: open - Opened by hanpengluo over 1 year ago - 2 comments
Labels: question

#321 - Warning: Sample has a non-default paired-end layout!

Issue - State: open - Opened by z1242099843 over 1 year ago - 2 comments

#320 - Short insert size

Issue - State: closed - Opened by oghzzang over 1 year ago - 4 comments
Labels: question

#319 - add option to delly filter to soft-filter variants

Pull Request - State: closed - Opened by lindenb over 1 year ago

#318 - Feature request: Delly filter + soft filter.

Issue - State: closed - Opened by lindenb over 1 year ago - 1 comment

#317 - Get STRAND INFO in the vcf output

Issue - State: open - Opened by Sreelekshmi-291 over 1 year ago - 1 comment

#316 - fatal error: boost/graph/adjacency_list.hpp

Issue - State: closed - Opened by volcano1998 over 1 year ago

#315 - FATAL: kernel too old

Issue - State: closed - Opened by xiekunwhy over 1 year ago - 1 comment

#314 - Understanding DELLY (Version: 0.9.1) output VCF file for BND

Issue - State: closed - Opened by tanbiswas almost 2 years ago - 3 comments
Labels: question

#313 - 、

Issue - State: closed - Opened by Yixiangzhang1996 almost 2 years ago

#312 - How to call and genotype only with split reads?

Issue - State: closed - Opened by FrankFeng2022 almost 2 years ago - 4 comments
Labels: question

#311 - Consensus sequences

Issue - State: open - Opened by ceromova almost 2 years ago - 5 comments
Labels: question

#310 - Segmentation fault (core dumped) delly cnv

Issue - State: open - Opened by RochaLAJ almost 2 years ago - 5 comments
Labels: bug

#309 - Redirecting temporary directory

Issue - State: closed - Opened by kimin0402 almost 2 years ago - 2 comments

#308 - "Alignment file is missing" error when the input bam file is compressed using PetaGene

Issue - State: closed - Opened by ilavidas almost 2 years ago - 2 comments
Labels: enhancement

#307 - Compile error for multi-threading mode

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

#306 - Warning: Sample has a non-default paired-end layout!

Issue - State: open - Opened by liujiaxin7 almost 2 years ago - 6 comments
Labels: question

#304 - make all error

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

#303 - Delly bcf output annotation

Issue - State: closed - Opened by jiaren-zhang about 2 years ago - 1 comment

#302 - Strange distribution of QUAL values

Issue - State: closed - Opened by miyakokodama about 2 years ago - 1 comment

#301 - Feature request: option to use multiple types at once

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

#300 - About SV detection of Pacbio Hifi

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

#299 - There is a big difference between PE,SR and DV,RV. Why?

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

#298 - core dumped with delly merge

Issue - State: closed - Opened by chenlu-Liu about 2 years ago - 6 comments

#297 - segmentation fault at split reads assembly point

Issue - State: closed - Opened by skose82 about 2 years ago - 3 comments

#296 - Another sample stuck at SV annotation

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

#295 - About delly filter -s samples.tsv

Issue - State: open - Opened by ClarenceHsiang about 2 years ago - 6 comments

#294 - A question about merge parameter -p

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

#293 - Difference between germline SV vs germline CNV?

Issue - State: closed - Opened by kvn95ss over 2 years ago - 3 comments

#292 - All runs stuck at 50% Split-read assembly

Issue - State: closed - Opened by andreaswallberg over 2 years ago - 2 comments
Labels: question

#291 - multi-threading mode compilation errors

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

#290 - SR query

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

#289 - interpretation of direction values not matching known logic

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

#288 - Errors building with Spack

Issue - State: closed - Opened by justbennet over 2 years ago - 2 comments
Labels: wontfix

#287 - Germline SV calling (Questions)

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

#286 - Delly output to stdout

Issue - State: closed - Opened by fgvieira over 2 years ago - 5 comments
Labels: enhancement

#285 - delly2 outputs duplicate results?

Issue - State: closed - Opened by GuoYu-Peng over 2 years ago - 1 comment
Labels: question

#284 - compilation terminated

Issue - State: closed - Opened by CLAIRE-cuhk over 2 years ago - 4 comments
Labels: question

#283 - Can delly be used with viruses?

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

#282 - Is it possible to access an alignment file from an S3 bucket?

Issue - State: open - Opened by james-guevara over 2 years ago - 5 comments
Labels: enhancement

#281 - DELLY with conda

Issue - State: closed - Opened by josiejenyne over 2 years ago - 2 comments
Labels: question

#280 - Speed Issue Delly

Issue - State: closed - Opened by skose82 over 2 years ago - 1 comment

#279 - Speed Issue Delly

Issue - State: closed - Opened by skose7 over 2 years ago

#278 - Interpretation of Delly SV Call output

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

#276 - symbol lookup error with bioconda delly 0.9.1

Issue - State: closed - Opened by jdm204 over 2 years ago - 2 comments

#275 - Germline SV calling Whole exome sequence

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

#274 - Delly installation in ubuntu 9.3.0-17ubuntu1~20.04

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

#273 - Output BAM with tags to associate reads back to SV calls?

Issue - State: closed - Opened by nh13 over 2 years ago - 6 comments

#272 - Starting from which version does Delly2 specify

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

#271 - Evidence reads

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

#270 - Unexpected genotyping and filtering results

Issue - State: closed - Opened by MathijsSanders almost 3 years ago - 3 comments
Labels: bug

#269 - Mappability map for T2T CHM13

Issue - State: closed - Opened by davidebolo1993 almost 3 years ago - 3 comments

#268 - Multithreading with Conda version

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

#267 - Error of Delly Segmentation fault(core dumped)

Issue - State: closed - Opened by pabloangulo7 almost 3 years ago - 15 comments

#266 - Inquiry about -x excl file and option

Issue - State: closed - Opened by OZTaekOppa almost 3 years ago - 5 comments