fritzsedlazeck/spectre issues and pull requests

#39 - Question regarding min_cnv_length parameter

Issue - State: open - Opened by reshu23 8 days ago

#38 - Coordinates of CNV position

Issue - State: open - Opened by reshu23 16 days ago - 2 comments

#37 - Output Bed file description

Issue - State: closed - Opened by reshu23 23 days ago - 2 comments

#36 - Minimum CNV length must be greater then 10000 base pairs

Issue - State: open - Opened by fidibidi about 1 month ago - 1 comment

#35 - No .vcf.gz/.vcf.gz.tbi file generated when no variants are reported

Issue - State: closed - Opened by SergeWielhouwer about 1 month ago - 2 comments

#34 - using SNV/SNP file with spectre in tumour samples

Issue - State: open - Opened by eesiribloom about 1 month ago - 2 comments

#33 - No cnv found in teh vcf

Issue - State: open - Opened by pcr876 about 1 month ago - 2 comments

#32 - Modernise a bit.

Pull Request - State: closed - Opened by kylematoba 2 months ago - 1 comment

#31 - KeyError "MT"

Issue - State: closed - Opened by sandratra-rab 2 months ago - 3 comments

#30 - Usage recommendations, confusion about mosdepth example command

Issue - State: open - Opened by SergeWielhouwer 3 months ago - 3 comments

#29 - KeyError: '2'

Issue - State: closed - Opened by pcr876 3 months ago - 1 comment

#28 - Question regarding the blacklist for specific genome builds

Issue - State: open - Opened by bartcharbon 4 months ago - 1 comment

#27 - Illegal DP FORMAT field in output

Issue - State: closed - Opened by bartcharbon 4 months ago - 2 comments

#26 - Empty result creates vcf instead of vcf.gz

Issue - State: closed - Opened by bartcharbon 4 months ago - 1 comment
Labels: bug

#25 - Big difference between results of qdnaseq and spectre

Issue - State: open - Opened by EugeneKim76 5 months ago - 3 comments

#24 - RecursionError: maximum recursion depth exceeded in comparison

Issue - State: open - Opened by adbeggs 5 months ago - 1 comment
Labels: bug

#23 - Adaptive sequencing CNV calling

Issue - State: open - Opened by adbeggs 5 months ago - 1 comment

#22 - About min_cnv_len

Issue - State: closed - Opened by EugeneKim76 5 months ago - 1 comment

#21 - Crash on SNV module

Issue - State: open - Opened by adbeggs 6 months ago - 3 comments

#20 - Question about QUAL, GQ, FILTER and SVSUPPORT

Issue - State: closed - Opened by JakeHagen 6 months ago - 8 comments
Labels: bug

#19 - Skips all het SNV sites because deepvariant uses Number=A for the VAF format field.

Issue - State: open - Opened by JakeHagen 7 months ago - 3 comments

#18 - Not providing a blacklist leads to stack trace

Issue - State: closed - Opened by mp15 7 months ago - 2 comments

#17 - Empty vcf file produced instead of vcf.gz file

Issue - State: closed - Opened by Tintest 7 months ago - 6 comments

#16 - False positives CNV called for chrX in men

Issue - State: closed - Opened by Tintest 7 months ago

#15 - Error with --population parameter

Issue - State: closed - Opened by Tintest 7 months ago - 1 comment
Labels: bug

#14 - Error due to undesirable use of an alternative contig of the reference genome

Issue - State: closed - Opened by Tintest 7 months ago - 1 comment
Labels: bug

#13 - CNLOH determination fails

Issue - State: closed - Opened by adbeggs 7 months ago - 5 comments
Labels: bug

#12 - CNV plotting fails

Issue - State: closed - Opened by adbeggs 7 months ago
Labels: bug

#11 - Spectre needs a blacklist or crashes out

Issue - State: closed - Opened by adbeggs 7 months ago
Labels: bug

#10 - RemoveN's

Issue - State: closed - Opened by adbeggs 7 months ago
Labels: bug

#9 - Odd behaviour in VCF and BED files - duplicate entries

Issue - State: closed - Opened by adbeggs 8 months ago - 2 comments
Labels: bug

#8 - CNV caller min_cnv_len

Issue - State: closed - Opened by VICTO160 8 months ago - 1 comment
Labels: bug, documentation

#7 - Refactor modules to support installing directly with pip

Pull Request - State: closed - Opened by edawson about 1 year ago

#6 - blacklist question

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

#5 - Update README.md

Pull Request - State: closed - Opened by wdecoster about 1 year ago

#4 - Feature Request - tumour-normal calling

Issue - State: open - Opened by adbeggs about 1 year ago - 2 comments
Labels: enhancement

GitHub / fritzsedlazeck/spectre issues and pull requests