Ecosyste.ms: Issues

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GitHub / illumina/cyrius issues and pull requests

#40 - Warning message

Issue - State: open - Opened by diegomd90 about 1 year ago - 3 comments

#40 - Warning message

Issue - State: open - Opened by diegomd90 about 1 year ago - 3 comments

#39 - Installing Cyrius using pip for ease of use with other python tools

Issue - State: open - Opened by timsanford about 1 year ago - 3 comments

#39 - Installing Cyrius using pip for ease of use with other python tools

Issue - State: open - Opened by timsanford about 1 year ago - 3 comments

#38 - improved support for index file at non-traditional locations

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

#38 - improved support for index file at non-traditional locations

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

#37 - Using Cyrius within other tools/workflow management

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

#37 - Using Cyrius within other tools/workflow management

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

#36 - snp_count.py:127: UserWarning, haplotype.py:70: UserWarning

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

#36 - snp_count.py:127: UserWarning, haplotype.py:70: UserWarning

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

#35 - How to correct "ZeroDivisionError: division by zero" ?

Issue - State: closed - Opened by PavitaKae over 1 year ago - 2 comments

#35 - How to correct "ZeroDivisionError: division by zero" ?

Issue - State: closed - Opened by PavitaKae over 1 year ago - 2 comments

#34 - WES

Issue - State: closed - Opened by shahed9s almost 2 years ago - 1 comment

#34 - WES

Issue - State: closed - Opened by shahed9s almost 2 years ago - 1 comment

#32 - Questions about odd genotypes

Issue - State: closed - Opened by anh151 almost 2 years ago - 4 comments

#32 - Questions about odd genotypes

Issue - State: closed - Opened by anh151 almost 2 years ago - 4 comments

#31 - Unknown variants?

Issue - State: closed - Opened by yebinkim17 about 2 years ago - 2 comments

#31 - Unknown variants?

Issue - State: closed - Opened by yebinkim17 about 2 years ago - 2 comments

#30 - processing steps to be on the lookout for in a CRAM?

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

#30 - processing steps to be on the lookout for in a CRAM?

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

#29 - fetch called on bamfile without index?

Issue - State: closed - Opened by yebinkim17 about 2 years ago - 2 comments

#29 - fetch called on bamfile without index?

Issue - State: closed - Opened by yebinkim17 about 2 years ago - 2 comments

#28 - 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte

Issue - State: open - Opened by mdAdnn about 2 years ago - 9 comments

#28 - 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte

Issue - State: open - Opened by mdAdnn about 2 years ago - 9 comments

#27 - Panel data

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

#27 - Panel data

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

#26 - WGS only?

Issue - State: closed - Opened by JARM89 over 2 years ago - 7 comments

#26 - WGS only?

Issue - State: closed - Opened by JARM89 over 2 years ago - 7 comments

#25 - Question about "None" phenotype

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

#25 - Question about "None" phenotype

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

#24 - ValueError: invalid contig `22`

Issue - State: closed - Opened by Giuseppe1995 over 2 years ago - 2 comments

#24 - ValueError: invalid contig `22`

Issue - State: closed - Opened by Giuseppe1995 over 2 years ago - 2 comments

#23 - new version?

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

#23 - new version?

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

#22 - Issue with file path error?

Issue - State: open - Opened by joseph-yclam about 3 years ago - 3 comments

#22 - Issue with file path error?

Issue - State: open - Opened by joseph-yclam about 3 years ago - 3 comments

#21 - Error Running CRAM Files

Issue - State: closed - Opened by pmbock1 about 3 years ago - 4 comments

#21 - Error Running CRAM Files

Issue - State: closed - Opened by pmbock1 about 3 years ago - 4 comments

#20 - Using cyrius on a specific panel of genes not WGS

Issue - State: closed - Opened by CYP2D about 3 years ago - 1 comment

#20 - Using cyrius on a specific panel of genes not WGS

Issue - State: closed - Opened by CYP2D about 3 years ago - 1 comment

#19 - troubleshooting "no call" outputs for samples with coverage above 30X

Issue - State: closed - Opened by mgonzalezporta about 3 years ago - 4 comments

#19 - troubleshooting "no call" outputs for samples with coverage above 30X

Issue - State: closed - Opened by mgonzalezporta about 3 years ago - 4 comments

#18 - underscores in diplotype calls

Issue - State: closed - Opened by mgonzalezporta about 3 years ago - 4 comments

#18 - underscores in diplotype calls

Issue - State: closed - Opened by mgonzalezporta about 3 years ago - 4 comments

#17 - Minor bug in target variants for GRch37

Issue - State: closed - Opened by benz888-tech about 3 years ago - 2 comments

#17 - Minor bug in target variants for GRch37

Issue - State: closed - Opened by benz888-tech about 3 years ago - 2 comments

#16 - Calling on Cyrius test data

Issue - State: closed - Opened by benediktusrayo-nala about 3 years ago - 1 comment

#16 - Calling on Cyrius test data

Issue - State: closed - Opened by benediktusrayo-nala about 3 years ago - 1 comment

#15 - Conda package?

Issue - State: open - Opened by kokyriakidis about 3 years ago - 2 comments

#15 - Conda package?

Issue - State: open - Opened by kokyriakidis about 3 years ago - 2 comments

#14 - Alternate and Reference Read Count Output Format

Issue - State: closed - Opened by benediktusrayo-nala about 3 years ago - 1 comment

#14 - Alternate and Reference Read Count Output Format

Issue - State: closed - Opened by benediktusrayo-nala about 3 years ago - 1 comment

#13 - interpreting d67_snp_* fields in json output

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

#13 - interpreting d67_snp_* fields in json output

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

#12 - Sample specific error

Issue - State: closed - Opened by holtjma over 3 years ago - 7 comments

#12 - Sample specific error

Issue - State: closed - Opened by holtjma over 3 years ago - 7 comments

#11 - UnicodeDecodeError

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

#11 - UnicodeDecodeError

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

#10 - support non-standard index names

Pull Request - State: closed - Opened by cariaso almost 4 years ago - 1 comment

#10 - support non-standard index names

Pull Request - State: closed - Opened by cariaso almost 4 years ago - 1 comment

#9 - Alignment to PGx regions only

Issue - State: closed - Opened by kokyriakidis almost 4 years ago - 5 comments

#9 - Alignment to PGx regions only

Issue - State: closed - Opened by kokyriakidis almost 4 years ago - 5 comments

#8 - Minor update

Pull Request - State: closed - Opened by xiao-chen-xc almost 4 years ago

#8 - Minor update

Pull Request - State: closed - Opened by xiao-chen-xc almost 4 years ago

#7 - RuntimeWarning: divide by zero encountered in true_divide

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

#6 - support remote URIs

Pull Request - State: closed - Opened by cariaso almost 4 years ago - 5 comments

#5 - Is there a way to use just a part of cram/bam file to get not-None Cyrius result?

Issue - State: closed - Opened by muzic194 almost 4 years ago - 2 comments

#4 - "None" genotypes with GATK4 best practices BAM/CRAMs

Issue - State: closed - Opened by mgonzalezporta about 4 years ago - 11 comments

#3 - Updated Cyrius to call all star alleles (up to *139)

Pull Request - State: closed - Opened by xiao-chen-xc over 4 years ago

#2 - Calling on HG00463 results in s/w crash.

Issue - State: open - Opened by iamh2o over 4 years ago - 1 comment

#1 - Recommended upstream alignment

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