fritzsedlazeck/survivor issues and pull requests

#96 - SURVIVOR filter based on AF has no effect

Issue - State: open - Opened by oleraj about 5 years ago - 4 comments

#95 - Multiple samples in one VCF

Issue - State: closed - Opened by alexmathieu about 5 years ago - 2 comments

#94 - GL missing after merging

Issue - State: closed - Opened by usevani over 5 years ago - 3 comments

#93 - SURVIVOR with paragraph

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

#92 - GRIDSS support

Issue - State: open - Opened by d-cameron over 5 years ago - 14 comments

#91 - SURVIVOR wrong merge

Issue - State: closed - Opened by Litterlemon over 5 years ago - 3 comments

#90 - Assemblytics to VCF with SV name leftover

Issue - State: closed - Opened by RenzoTale88 over 5 years ago - 3 comments

#89 - Venn

Issue - State: closed - Opened by biomichal over 5 years ago - 11 comments

#88 - SURVIVOR merging to wrong svtypes.

Issue - State: closed - Opened by unique379r over 5 years ago - 16 comments

#87 - Finding CNVs that do not intersect/merge with reference set

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

#86 - Will survivor merge two calls if they have different genotyping?

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

#85 - Merged calls: variants present in none of the samples

Issue - State: closed - Opened by CWYuan08 over 5 years ago - 21 comments

#84 - Merge SVLEN issue

Issue - State: closed - Opened by WEClarke over 5 years ago - 9 comments

#83 - pos is 0 in merged vcf

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

#82 - Can SURVIVOR Merge PBSV results？

Issue - State: closed - Opened by biomichal over 5 years ago - 11 comments
Labels: enhancement

#81 - Problem Merging SVs of 10X with delly, lumpy and breakdancer.

Issue - State: closed - Opened by unique379r over 5 years ago - 14 comments

#80 - SURVIVOR merge and size-based distance estimation

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

#79 - streambuf/overflow shouln't advance the setg

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

#78 - fix buf in underflow

Pull Request - State: closed - Opened by lindenb over 5 years ago - 3 comments

#77 - error when installing SURVIVOR

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

#76 - fix includes for https://github.com/fritzsedlazeck/SURVIVOR/issues/75

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

#75 - Compilation problem (make)

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

#74 - fix colon in manta id

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

#73 - support for gzip stream

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

#72 - SIGSEGV with manta data

Issue - State: closed - Opened by lindenb over 5 years ago - 3 comments
Labels: enhancement

#71 - how SURVIVOR merge works in case of DEL ?

Issue - State: closed - Opened by unique379r over 5 years ago - 1 comment

#70 - SURVIVOR merge GT

Issue - State: closed - Opened by apaul7 over 5 years ago - 8 comments

#69 - Intersection of multiple vcfs

Issue - State: closed - Opened by unique379r over 5 years ago - 6 comments

#68 - SURVIVOR filter using bed

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

#67 - Genotyping supported in SURVIVOR?

Issue - State: closed - Opened by cedkid over 5 years ago - 6 comments

#66 - SURVIVOR merge files outputs no sites

Issue - State: closed - Opened by complexgenome almost 6 years ago - 9 comments

#65 - Merge strategy multiple samples and tools

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

#64 - Survivor limits?

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

#63 - SURVIVOR merge takes cross chromosomes to merge

Issue - State: closed - Opened by unique379r almost 6 years ago - 8 comments

#62 - Limit size of variants

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

#61 - Same position in two different lines

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

#60 - somatic SV calls not merging correctly

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

#59 - merge produces invalid VCF when input VCFs contain a common sample name

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

#58 - merge produces invalid VCF when used on Manta VCFs

Issue - State: closed - Opened by Lenbok almost 6 years ago - 5 comments

#57 - character other than ACTG in simulated reads

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

#56 - Large SURVIVOR merge operation

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

#55 - Wrong merge outputs

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

#54 - SURVIVOR merge question

Issue - State: closed - Opened by tiplud almost 6 years ago - 27 comments

#53 - vcftobed info

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

#52 - SURVIVOR merge produces unsorted VCFs

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

#51 - Improve compliance of "merge" output to VCF specification

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

#50 - VCF merge about strand

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

#49 - merge vcf : Information for DR

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

#48 - SV position

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

#47 - SURVIVOR merge AVGLEN positive when SVTYPE=DEL

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

#46 - Duplication max length does not work

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

#45 - SVTYPE DUP merging into NA

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

#44 - SURVIVOR merge

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

#43 - Details about simSV parameter

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

#42 - Compiling error

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

#41 - using NA12878_nano_error_profile_bwa.txt

Issue - State: closed - Opened by ramcn about 6 years ago - 5 comments

#40 - Detail about SURVIVOR simSV

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

#39 - SURVIVOR scanreads output doesn't contain any information.

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

#38 - filter by min SV size using proportion of SV overlapping

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

#37 - vcftobed use AVGLEN values in INFO column

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

#36 - SURVIVOR filter removing all SV's and receiving error message

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

#35 - is there a way to simulate large deletions by simSV?

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

#34 - merge strategy

Issue - State: closed - Opened by shishuo16 over 6 years ago - 1 comment

#33 - Terminate program as it could not find a non overlapping region

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

#32 - options for merge

Issue - State: closed - Opened by shishuo16 over 6 years ago - 4 comments

#31 - merge vcf SVTYPE

Issue - State: closed - Opened by tgong1 over 6 years ago - 2 comments

#30 - merge vcf: some entries failed to merge

Issue - State: closed - Opened by arkyl over 6 years ago - 5 comments

#29 - cend.first and cend.second in combine_svs.cpp

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

#28 - SVTYPE <NA>

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

#27 - SURVIVOR merge vcf files

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

#26 - Assemblytics output to vcf

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

#25 - some request on genotyping

Issue - State: closed - Opened by ytguojian over 6 years ago - 12 comments

#24 - somethings not understand

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

#23 - fix typo

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

#22 - Minimum number of supporting caller

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

#21 - SURVIVOR simreads

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

#20 - row names in R script crashing

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

#19 - SURVIVOR scanreads does not work

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

#18 - Feature Request: testing against a control SV set

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

#17 - error when running SURVIVOR merge

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

#16 - Dropping INS during vcftobed

Issue - State: closed - Opened by Phillip-a-richmond over 6 years ago - 2 comments

#15 - sample names instead of file names (merge tool)

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

#14 - Reciprocal overlap

Issue - State: closed - Opened by Phillip-a-richmond almost 7 years ago - 21 comments

#13 - improve parameter interface.

Issue - State: closed - Opened by fritzsedlazeck almost 7 years ago - 1 comment
Labels: enhancement

#12 - Simulating NGS reads from SV introduced fasta file

Issue - State: closed - Opened by MehmetGoktay almost 7 years ago - 2 comments

#11 - Minor systematic bias on small deletions/insertions

Issue - State: closed - Opened by ctsa almost 7 years ago - 2 comments

#10 - SURVIVOR 10 issue

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

#9 - Venn vs. VCF event.

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

#8 - SURVIVOR stalls when reference FASTA lacks newlines

Issue - State: closed - Opened by lcoombe about 7 years ago - 8 comments
Labels: enhancement

#7 - Please consider adding descriptive comments and a short summary

Issue - State: closed - Opened by sinamomken about 7 years ago - 5 comments

#6 - Interpretation of sv-simulated bed file

Issue - State: closed - Opened by svm-zhang over 7 years ago - 13 comments

#5 - Error when installing SURVIVOR: undefined references

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

#4 - Do you know if anyone has tried adapting this for array based CNV calling?

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

#3 - misleading short program description

Issue - State: closed - Opened by 0xaf1f over 7 years ago - 6 comments

#2 - Extend SURVIVOR for strand tag

Issue - State: closed - Opened by fritzsedlazeck about 8 years ago - 1 comment

#1 - How should start, end, and size of insertions be compared?

Issue - State: closed - Opened by jzook about 8 years ago - 3 comments

GitHub / fritzsedlazeck/survivor issues and pull requests