ssadedin ximmer issues - Githubissues

ssadedin / ximmer

Ximmer is a system for CNV calling on exome and targeted genomic sequencing

http://ssadedin.github.io/ximmer/

GNU Lesser General Public License v2.1

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issues

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Extract lumpy PE & SU info from vcf and pass it through to ximmer local_combined_cnvs.json output

#43 TacModd closed 2 weeks ago
1
update Dockerfile

#42 tgambin opened 2 years ago
2
create_analysable_targets not working

#41 brianlucla opened 2 years ago
3
Installation errors with xhmm

#40 longfei-stat opened 2 years ago
2
How many bam do I need ?

#39 dridk opened 3 years ago
0
Feat register wgs vcf

#38 cvlvxi closed 1 year ago
0
java error in the database download

#37 flapa86 opened 3 years ago
0
Failure in CNVDiagram produces empty js file

#36 ssadedin opened 3 years ago
0
Chromosome * is not analysable by CODEX and many more

#35 vinzenzmay opened 4 years ago
0
KILLED error when running ximmer through docker

#34 emyli14 opened 4 years ago
0
install script is missing

#33 johnemajor opened 4 years ago
0
allow HGFA to be set in local config

#32 bpow opened 4 years ago
0
Add '-L' option to curl

#31 bpow opened 4 years ago
0
java.lang.RuntimeException: After comparing the samples specified in the 'samples' block with the available BAM files, no samples remain to analyse

#30 hkrzystek closed 4 years ago
0
config. java.lang.IllegalArgumentException: Please set the HGFA parameter to your human genome reference in the config file at: /usr/local/ximmer/eval/pipeline/config.groovy Error

#29 hkrzystek opened 4 years ago
5
Docker - Tables are not installed

#28 bopohdr closed 4 years ago
2
Upgrade to hg38

#27 bopohdr closed 4 years ago
6
startup failed 107: expecting '*', found '<EOF>' @ line 107, column 1.

#26 biobai opened 5 years ago
0
Expose XIMMER_REF in config.groovy rather than a env variable for docker run

#25 sclan opened 5 years ago
0
ERROR: Sample CREATE_INDEX=true appears in more than one BAM file

#24 kunstner opened 5 years ago
0
ERROR: analysis pipeline did not produce expected analysed target region BED (running through docker)

#23 xexpanderx opened 5 years ago
3
Empty diagram for CNV without gene annotation

#22 pixuenan opened 5 years ago
0
Wrong coverage block highlight on the cnv diagram

#21 pixuenan opened 5 years ago
0
docker install problem

#20 jchenpku opened 5 years ago
0
Docker without pandas

#19 pixuenan closed 5 years ago
2
High false positive number and x-replacement simulation failure

#18 pixuenan opened 5 years ago
4
Analysis failed - getting JAVA errors:groovy.lang.MissingMethodException: No signature of method: groovy.util.ConfigObject.MOPs()

#17 SafinaAr opened 5 years ago
16
Error at install

#16 gybeata opened 5 years ago
5
Error: java.lang Invalid reference index -1

#15 bopohdr closed 4 years ago
5
Failed analysis due to problems with finding JAVA_home

#14 bopohdr closed 4 years ago
2
Analysis failed

#13 natashapinto opened 6 years ago
2
Unable to run Ximmer

#12 natashapinto closed 5 years ago
4
Canot get ximmer to run on Ubuntu 16.04

#11 chapplec opened 6 years ago
7
parameter to take in count relatedness in data

#10 gybeata opened 6 years ago
1
Error

#9 SamKap-2 opened 6 years ago
2
Dockerfile enhancements

#8 0xaf1f opened 6 years ago
0
plans to host on dockerhub?

#7 0xaf1f opened 6 years ago
5
Using and underscore in an analysisconfig results in wrongly labeled ROC curve

#6 ssadedin opened 6 years ago
0
Diagrams of CNVs not showing in report

#5 ssadedin closed 6 years ago
0
Need a loading spinner for the Runs tab

#4 ssadedin opened 6 years ago
0
overlapping labels in summary plots

#3 ssadedin opened 6 years ago
0
Should check configuration: callers included in analyses must overlap configured callers

#2 ssadedin opened 7 years ago
0
BAM preparations

#1 dezzan opened 8 years ago
1