illumina/strelka issues and pull requests

#100 - which tier should be used to calculate variant allele frequencies

Issue - State: closed - Opened by qindan2008 over 5 years ago - 2 comments

#100 - which tier should be used to calculate variant allele frequencies

Issue - State: closed - Opened by qindan2008 over 5 years ago - 2 comments

#99 - Unknown error in first step of Strelka

Issue - State: closed - Opened by beginner984 over 5 years ago - 19 comments

#99 - Unknown error in first step of Strelka

Issue - State: closed - Opened by beginner984 over 5 years ago - 19 comments

#98 - strelka2 and tumour only calling

Issue - State: closed - Opened by sbilobram over 5 years ago - 7 comments

#98 - strelka2 and tumour only calling

Issue - State: closed - Opened by sbilobram over 5 years ago - 7 comments

#97 - gVCF error?

Issue - State: closed - Opened by wangshun1121 almost 6 years ago - 9 comments

#97 - gVCF error?

Issue - State: closed - Opened by wangshun1121 almost 6 years ago - 9 comments

#96 - double line entries for indels.

Issue - State: open - Opened by curtisjamison almost 6 years ago - 1 comment

#96 - double line entries for indels.

Issue - State: open - Opened by curtisjamison almost 6 years ago - 1 comment

#95 - Somatic SNVs Near Homopolymers

Issue - State: open - Opened by DarioS almost 6 years ago - 3 comments

#95 - Somatic SNVs Near Homopolymers

Issue - State: open - Opened by DarioS almost 6 years ago - 3 comments

#94 - Permit Input Sample Naming

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

#94 - Permit Input Sample Naming

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

#93 - Resource Guide

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

#93 - Resource Guide

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

#92 - Output realigned BAM doesn't output BAM file

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

#92 - Output realigned BAM doesn't output BAM file

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

#91 - Extra Example Desired for Joint Analysis

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

#91 - Extra Example Desired for Joint Analysis

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

#90 - What is the definition of false positive regions?

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

#90 - What is the definition of false positive regions?

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

#89 - strelka2 very slow and trashing disk on ext4

Issue - State: open - Opened by derijkp almost 6 years ago - 11 comments

#89 - strelka2 very slow and trashing disk on ext4

Issue - State: open - Opened by derijkp almost 6 years ago - 11 comments

#88 - Update README File

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

#88 - Update README File

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

#87 - Which read tier is used to determine PASS

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

#87 - Which read tier is used to determine PASS

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

#86 - the question of MAPQ

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

#86 - the question of MAPQ

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

#85 - SmallAssembler vs IterativeAssembler

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

#85 - SmallAssembler vs IterativeAssembler

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

#84 - Version 2.8.0 as in Illumina Tumor app 5.0 is required

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

#84 - Version 2.8.0 as in Illumina Tumor app 5.0 is required

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

#83 - How could avoid contamination model？

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

#83 - How could avoid contamination model？

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

#82 - Got WARNING and ERROR info when using StrelkaGermlineWorkflow on multi-samples

Issue - State: closed - Opened by huangl07 almost 6 years ago - 6 comments

#82 - Got WARNING and ERROR info when using StrelkaGermlineWorkflow on multi-samples

Issue - State: closed - Opened by huangl07 almost 6 years ago - 6 comments

#81 - TAR field

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

#81 - TAR field

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

#80 - Extreme runtime and no results for somatic T/N WGS calling using Strelka

Issue - State: closed - Opened by rxliu almost 6 years ago - 10 comments

#80 - Extreme runtime and no results for somatic T/N WGS calling using Strelka

Issue - State: closed - Opened by rxliu almost 6 years ago - 10 comments

#79 - SomaticEVS threshold

Issue - State: closed - Opened by JunyanZH6 about 6 years ago - 1 comment

#79 - SomaticEVS threshold

Issue - State: closed - Opened by JunyanZH6 about 6 years ago - 1 comment

#78 - Intermediate VCF file availability

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

#78 - Intermediate VCF file availability

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

#77 - minimum mapping quality for variant calls?

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

#77 - minimum mapping quality for variant calls?

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

#76 - No indels found using strelka2

Issue - State: closed - Opened by ysbioinfo about 6 years ago - 8 comments

#76 - No indels found using strelka2

Issue - State: closed - Opened by ysbioinfo about 6 years ago - 8 comments

#75 - genotype likelihoods (PL) for reference calls with --forcedGT

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

#75 - genotype likelihoods (PL) for reference calls with --forcedGT

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

#74 - Hom alt GT reported incorrectly

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

#74 - Hom alt GT reported incorrectly

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

#73 - Genotype field is missing in VCF file

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

#73 - Genotype field is missing in VCF file

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

#72 - Impact of not pre-running Manta on somatic indels calls

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

#72 - Impact of not pre-running Manta on somatic indels calls

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

#71 - Only got very few SNVs using Strelka2

Issue - State: closed - Opened by fredsamhaak about 6 years ago - 9 comments

#71 - Only got very few SNVs using Strelka2

Issue - State: closed - Opened by fredsamhaak about 6 years ago - 9 comments

#70 - Problem with long insertions in realigned RNASeq BAM files

Issue - State: closed - Opened by mozack about 6 years ago - 7 comments

#70 - Problem with long insertions in realigned RNASeq BAM files

Issue - State: closed - Opened by mozack about 6 years ago - 7 comments

#69 - Strelka2 fails when running with jobs > 1

Issue - State: closed - Opened by ahwanpandey about 6 years ago - 8 comments

#69 - Strelka2 fails when running with jobs > 1

Issue - State: closed - Opened by ahwanpandey about 6 years ago - 8 comments

#68 - Error: skipping alignment for read outside of buffer range

Issue - State: closed - Opened by rahulvrane about 6 years ago - 1 comment

#68 - Error: skipping alignment for read outside of buffer range

Issue - State: closed - Opened by rahulvrane about 6 years ago - 1 comment

#67 - Got WARNING and ERROR info when using StrelkaGermlineWorkflow on multi-samples

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

#67 - Got WARNING and ERROR info when using StrelkaGermlineWorkflow on multi-samples

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

#66 - Strict matching between FASTA and BAM can be problematic

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

#66 - Strict matching between FASTA and BAM can be problematic

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

#65 - Somatic AF 0%

Issue - State: closed - Opened by ATpoint about 6 years ago - 8 comments

#65 - Somatic AF 0%

Issue - State: closed - Opened by ATpoint about 6 years ago - 8 comments

#64 - Difference between Strelka2 INDELs with BED and without

Issue - State: closed - Opened by looxon93 about 6 years ago - 1 comment

#64 - Difference between Strelka2 INDELs with BED and without

Issue - State: closed - Opened by looxon93 about 6 years ago - 1 comment

#63 - Performance issues on high depth amplicon data

Issue - State: open - Opened by jaudoux over 6 years ago - 2 comments

#63 - Performance issues on high depth amplicon data

Issue - State: open - Opened by jaudoux over 6 years ago - 2 comments

#62 - Inconsistant depth of result

Issue - State: closed - Opened by ray1919 over 6 years ago - 3 comments

#62 - Inconsistant depth of result

Issue - State: closed - Opened by ray1919 over 6 years ago - 3 comments

#61 - .fai not found due to symlink resolving

Issue - State: closed - Opened by DavyCats over 6 years ago - 2 comments
Labels: bug

#61 - .fai not found due to symlink resolving

Issue - State: closed - Opened by DavyCats over 6 years ago - 2 comments
Labels: bug

#60 - uncompressed/unindexed bed file for callRegions

Issue - State: open - Opened by DavyCats over 6 years ago - 1 comment
Labels: enhancement

#60 - uncompressed/unindexed bed file for callRegions

Issue - State: open - Opened by DavyCats over 6 years ago - 1 comment
Labels: enhancement

#59 - Multi-sample somatic calling

Issue - State: open - Opened by michaelnoe over 6 years ago - 5 comments
Labels: documentation

#59 - Multi-sample somatic calling

Issue - State: open - Opened by michaelnoe over 6 years ago - 5 comments
Labels: documentation

#58 - What is the correct input bam for Strelka2

Issue - State: open - Opened by BilyanaStoilova over 6 years ago - 9 comments

#58 - What is the correct input bam for Strelka2

Issue - State: open - Opened by BilyanaStoilova over 6 years ago - 9 comments

#57 - Difference of somatic InDel results between strelka and strelka2

Issue - State: closed - Opened by zhangnan0107 over 6 years ago - 6 comments

#57 - Difference of somatic InDel results between strelka and strelka2

Issue - State: closed - Opened by zhangnan0107 over 6 years ago - 6 comments

#56 - Strelka 2.9.3 FATAL_ERROR: Unexpected return value from htslib sam_itr_next function '-2' while attempting to read BAM/CRAM

Issue - State: open - Opened by burakonal89 over 6 years ago - 1 comment

#56 - Strelka 2.9.3 FATAL_ERROR: Unexpected return value from htslib sam_itr_next function '-2' while attempting to read BAM/CRAM

Issue - State: open - Opened by burakonal89 over 6 years ago - 1 comment

#55 - strelka-2 is frozen in CallGenome+callGenomeSegment

Issue - State: open - Opened by carleshf over 6 years ago - 1 comment

#55 - strelka-2 is frozen in CallGenome+callGenomeSegment

Issue - State: open - Opened by carleshf over 6 years ago - 1 comment

#54 - Python3

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

#54 - Python3

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

#53 - Regions of extremely high depth

Issue - State: open - Opened by tcashby over 6 years ago - 4 comments

#53 - Regions of extremely high depth

Issue - State: open - Opened by tcashby over 6 years ago - 4 comments

#52 - RNA-seq: Reached anomalous state during search for most likely exon alignment

Issue - State: closed - Opened by komalsrathi over 6 years ago - 8 comments

GitHub / illumina/strelka issues and pull requests