Ecosyste.ms: Issues

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GitHub / bcgsc/straglr issues and pull requests

#53 - Genotyping mononucleotide repeats

Issue - State: open - Opened by 18parkky 9 days ago

#52 - Issue in generating vcf file

Issue - State: open - Opened by MemoonaRasheed 25 days ago - 1 comment

#51 - Using Telomere-to-Telomere as reference

Issue - State: closed - Opened by Aarhus-kga about 2 months ago - 3 comments

#50 - type of file

Issue - State: closed - Opened by jawad9-11 2 months ago - 3 comments

#49 - TypeError: 'NoneType' object is not subscriptable

Issue - State: open - Opened by jawad9-11 2 months ago - 1 comment

#47 - --regions: a BED file containing regions to be used only in genome-scan

Issue - State: open - Opened by minw2828 2 months ago - 1 comment

#46 - Representing tandem repeats in VCF

Issue - State: open - Opened by dennishendriksen 3 months ago - 2 comments

#45 - Vcf does not get generated on Straglr version 1.5.0

Issue - State: closed - Opened by zaka-edd 3 months ago - 2 comments

#44 - genome-scan: IndexError: list index out of range

Issue - State: closed - Opened by lfearnley 4 months ago - 8 comments

#43 - IndexError: list index out of range

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

#42 - Discrepancy allele length and sequence

Issue - State: open - Opened by ljohansson 4 months ago - 16 comments

#41 - IndexError: list index out of range

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

#40 - Symbolic alleles in VCF output

Issue - State: open - Opened by bartcharbon 5 months ago - 7 comments

#39 - VCF output for hetrozygotes seems to be have incorrect GT's

Issue - State: closed - Opened by bartcharbon 5 months ago - 5 comments

#38 - Loci with multiple motifs at same position

Issue - State: open - Opened by christopher-schroeder 6 months ago - 4 comments

#37 - Interpretation on <output_prefix>.tsv

Issue - State: closed - Opened by HLHsieh 7 months ago - 1 comment

#36 - refactor: use dataclass for structured tsv reads

Pull Request - State: closed - Opened by lavafroth 8 months ago - 4 comments

#35 - Calling complex STR patterns

Issue - State: closed - Opened by bartcharbon 8 months ago - 1 comment

#34 - Not all loci in output bedfile

Issue - State: closed - Opened by ljohansson 8 months ago - 6 comments

#32 - Could Gender support and VCF output be added?

Issue - State: closed - Opened by bartcharbon 9 months ago - 5 comments

#31 - ValueError: invalid coordinates

Issue - State: closed - Opened by jyw-atgithub 9 months ago - 8 comments

#30 - Genotyping amplicons?

Issue - State: open - Opened by adbeggs 9 months ago - 1 comment

#29 - Why is detecting and genotyping Short Tandem Repeats (STRs) challenging?

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

#28 - Repeat Interruptions

Issue - State: open - Opened by stefandiederich 12 months ago - 11 comments

#27 - Problem with --trf_args

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

#27 - Problem with --trf_args

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

#26 - Problem with straglr_compare

Issue - State: closed - Opened by gspirito about 1 year ago - 6 comments

#26 - Problem with straglr_compare

Issue - State: closed - Opened by gspirito about 1 year ago - 6 comments

#25 - IndexError: list index out of range

Issue - State: closed - Opened by santoshe1 over 1 year ago - 3 comments

#25 - IndexError: list index out of range

Issue - State: closed - Opened by santoshe1 over 1 year ago - 3 comments

#24 - can‘t find STR

Issue - State: closed - Opened by sunmm0804 over 1 year ago - 2 comments

#23 - IndexError: list index out of range

Issue - State: closed - Opened by HLHsieh over 1 year ago - 4 comments

#22 - Question about the inconsistent motif between loci.bed and output.bed

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

#21 - Missing output

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

#20 - Error: malformed BED entry

Issue - State: closed - Opened by ziphra almost 2 years ago - 3 comments

#19 - An issue about complex STRs

Issue - State: open - Opened by fjmuzengyiheng almost 2 years ago - 12 comments

#18 - Error about "ValueError: start out of range (-265)"

Issue - State: closed - Opened by fjmuzengyiheng almost 2 years ago - 3 comments

#17 - Straglr not finding TR's that are definitely present in targeted sequencing data

Issue - State: closed - Opened by AliSTaylor about 2 years ago - 9 comments

#16 - An issue about reproducibility.

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

#15 - TRF options

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

#14 - About quality of detected VNTRs

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

#13 - Straglr seems to use multiple threads than specified threads

Issue - State: closed - Opened by Jesson-mark over 2 years ago - 24 comments

#12 - Update README.md

Pull Request - State: closed - Opened by zhemingfan over 2 years ago

#11 - TypeError: unsupported operand type(s) for /: 'str' and 'int'

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

#10 - STR count per strand

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

#9 - Conda release

Issue - State: closed - Opened by davidebolo1993 over 2 years ago - 3 comments

#8 - Stable release of staglr

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

#7 - What does parameter `min_support` mean in genotyping mode of Straglr?

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

#6 - Different results from different versions of straglr

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

#5 - Errors about running straglr to call tandem repeats

Issue - State: closed - Opened by LiShuhang-gif almost 3 years ago - 16 comments

#4 - Could I set the work directory for straglr?

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

#3 - Straglr could not find some TR that clearly existed

Issue - State: closed - Opened by LiShuhang-gif about 3 years ago - 10 comments

#2 - Understanding output

Issue - State: closed - Opened by MeiShu00 about 3 years ago - 4 comments

#1 - Error processing plasmid reads

Issue - State: closed - Opened by sabiqali about 3 years ago - 12 comments