illumina/pisces issues and pull requests

#81 - Calling variants with frequency lower than 1%

Issue - State: open - Opened by fa-vio about 1 month ago

#81 - Calling variants with frequency lower than 1%

Issue - State: open - Opened by fa-vio about 1 month ago

#80 - Is there any filtering required on Gemini output?

Issue - State: open - Opened by BrettLiddell 9 months ago - 2 comments

#80 - Is there any filtering required on Gemini output?

Issue - State: open - Opened by BrettLiddell 9 months ago - 2 comments

#79 - Confused with the last version releases

Issue - State: open - Opened by Manuel-DominguezCBG 9 months ago - 3 comments

#79 - Confused with the last version releases

Issue - State: open - Opened by Manuel-DominguezCBG 9 months ago - 3 comments

#78 - A fatal error was encountered. The library 'libhostpolicy.so' required to execute the application was not found in '/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/'.

Issue - State: closed - Opened by Manuel-DominguezCBG 9 months ago - 1 comment

#78 - A fatal error was encountered. The library 'libhostpolicy.so' required to execute the application was not found in '/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/'.

Issue - State: closed - Opened by Manuel-DominguezCBG 9 months ago - 1 comment

#77 - VennVcf 5.3.0.0 error: input string was not in a correct format

Issue - State: closed - Opened by fmazzarotto 12 months ago

#77 - VennVcf 5.3.0.0 error: input string was not in a correct format

Issue - State: closed - Opened by fmazzarotto 12 months ago

#76 - How to limit chr to 1-22,XY?

Issue - State: open - Opened by hfl112 about 1 year ago - 1 comment

#76 - How to limit chr to 1-22,XY?

Issue - State: open - Opened by hfl112 about 1 year ago - 1 comment

#75 - Can I disable the SB flag when not used?

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

#75 - Can I disable the SB flag when not used?

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

#74 - WRONG VF FOR LOW FREQUENCY VARIANTS

Issue - State: open - Opened by AriadnaColmeneroCobo over 1 year ago - 1 comment

#74 - WRONG VF FOR LOW FREQUENCY VARIANTS

Issue - State: open - Opened by AriadnaColmeneroCobo over 1 year ago - 1 comment

#73 - Read depth

Issue - State: open - Opened by ad2n15 over 2 years ago

#73 - Read depth

Issue - State: open - Opened by ad2n15 over 2 years ago

#72 - Scylla taking a very long time to process WES data / getting stuck

Issue - State: open - Opened by fmazzarotto over 2 years ago - 1 comment

#72 - Scylla taking a very long time to process WES data / getting stuck

Issue - State: open - Opened by fmazzarotto over 2 years ago - 1 comment

#71 - Bump Newtonsoft.Json from 9.0.2-beta2 to 13.0.1 in /src/lib/Alignment.IO

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#71 - Bump Newtonsoft.Json from 9.0.2-beta2 to 13.0.1 in /src/lib/Alignment.IO

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#70 - Bump Newtonsoft.Json from 9.0.2-beta2 to 13.0.1 in /src/lib/Common.IO

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#70 - Bump Newtonsoft.Json from 9.0.2-beta2 to 13.0.1 in /src/lib/Common.IO

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#69 - Creating a GenomeSize.xml for a soybean genome

Issue - State: open - Opened by brunabavelino over 2 years ago - 3 comments

#69 - Creating a GenomeSize.xml for a soybean genome

Issue - State: open - Opened by brunabavelino over 2 years ago - 3 comments

#68 - Pisces has different dp and no call？

Issue - State: open - Opened by user-tq over 2 years ago - 1 comment

#68 - Pisces has different dp and no call？

Issue - State: open - Opened by user-tq over 2 years ago - 1 comment

#67 - “No usable version of the libssl was found” on Linux

Issue - State: open - Opened by HEKntg almost 3 years ago - 1 comment

#67 - “No usable version of the libssl was found” on Linux

Issue - State: open - Opened by HEKntg almost 3 years ago - 1 comment

#66 - Can Pisces set the maximum coverage/sequence depth for SNV calling ?

Issue - State: open - Opened by ltongyu over 3 years ago - 1 comment

#66 - Can Pisces set the maximum coverage/sequence depth for SNV calling ?

Issue - State: open - Opened by ltongyu over 3 years ago - 1 comment

#65 - where can i download Scylla ?

Issue - State: open - Opened by worker000000 over 3 years ago - 1 comment

#65 - where can i download Scylla ?

Issue - State: open - Opened by worker000000 over 3 years ago - 1 comment

#64 - Stitcher don't have --intervals argument

Issue - State: closed - Opened by liuhongwei2018 over 3 years ago

#64 - Stitcher don't have --intervals argument

Issue - State: closed - Opened by liuhongwei2018 over 3 years ago

#63 - Does Pisces infer germline variants in tumor-only samples?

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

#63 - Does Pisces infer germline variants in tumor-only samples?

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

#62 - What's the difference between --collapse and --crushvcf options of Pisces

Issue - State: open - Opened by ShannonDaddy over 3 years ago - 2 comments

#62 - What's the difference between --collapse and --crushvcf options of Pisces

Issue - State: open - Opened by ShannonDaddy over 3 years ago - 2 comments

#61 - Get forward and reverse reads supportting the allele depth(refand alt)，respectively

Issue - State: open - Opened by diushiguzhi almost 4 years ago - 1 comment

#61 - Get forward and reverse reads supportting the allele depth(refand alt)，respectively

Issue - State: open - Opened by diushiguzhi almost 4 years ago - 1 comment

#60 - Gemini 5.3.0.0 Nullable object Error

Issue - State: open - Opened by ShannonDaddy almost 4 years ago - 1 comment

#60 - Gemini 5.3.0.0 Nullable object Error

Issue - State: open - Opened by ShannonDaddy almost 4 years ago - 1 comment

#59 - Pisces outputting 'Alignment error'

Issue - State: closed - Opened by fmazzarotto almost 4 years ago - 3 comments

#59 - Pisces outputting 'Alignment error'

Issue - State: closed - Opened by fmazzarotto almost 4 years ago - 3 comments

#58 - just FYI, for those who want to develop or debug Pisces on Linux..

Issue - State: open - Opened by tamsen almost 4 years ago - 5 comments

#58 - just FYI, for those who want to develop or debug Pisces on Linux..

Issue - State: open - Opened by tamsen almost 4 years ago - 5 comments

#57 - Does Pisces recognize the base quality score from PacBio HiFi reads?

Issue - State: open - Opened by turningA almost 4 years ago - 2 comments

#57 - Does Pisces recognize the base quality score from PacBio HiFi reads?

Issue - State: open - Opened by turningA almost 4 years ago - 2 comments

#56 - How the strand bias and R3x6 filter works in illumina platform?

Issue - State: open - Opened by N3ha247 about 4 years ago - 1 comment

#56 - How the strand bias and R3x6 filter works in illumina platform?

Issue - State: open - Opened by N3ha247 about 4 years ago - 1 comment

#55 - Gemini 5.2.11 does not complete - errors for different chromosomes

Issue - State: open - Opened by kotliary about 4 years ago - 4 comments

#55 - Gemini 5.2.11 does not complete - errors for different chromosomes

Issue - State: open - Opened by kotliary about 4 years ago - 4 comments

#54 - get forward and reverse support counts for Scylla merged variants

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

#54 - get forward and reverse support counts for Scylla merged variants

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

#53 - Running picard sam format converter for batch sample

Issue - State: open - Opened by zahraj242 over 4 years ago - 1 comment

#53 - Running picard sam format converter for batch sample

Issue - State: open - Opened by zahraj242 over 4 years ago - 1 comment

#52 - error running GATK workflow on local machine

Issue - State: open - Opened by zahraj242 over 4 years ago

#52 - error running GATK workflow on local machine

Issue - State: open - Opened by zahraj242 over 4 years ago

#51 - clustered snps can't be merged by scylla

Issue - State: open - Opened by ShannonDaddy over 4 years ago - 2 comments

#51 - clustered snps can't be merged by scylla

Issue - State: open - Opened by ShannonDaddy over 4 years ago - 2 comments

#50 - Hi, how to deal with multiple variants in a small region

Issue - State: open - Opened by ShannonDaddy over 4 years ago - 5 comments

#50 - Hi, how to deal with multiple variants in a small region

Issue - State: open - Opened by ShannonDaddy over 4 years ago - 5 comments

#49 - Targeting with bed files

Issue - State: open - Opened by ben-sanders almost 5 years ago - 1 comment

#49 - Targeting with bed files

Issue - State: open - Opened by ben-sanders almost 5 years ago - 1 comment

#48 - Empty output

Issue - State: open - Opened by jlee110 almost 5 years ago - 1 comment

#48 - Empty output

Issue - State: open - Opened by jlee110 almost 5 years ago - 1 comment

#47 - Limit RAM for GeminiMulti

Issue - State: open - Opened by dollinad about 5 years ago

#47 - Limit RAM for GeminiMulti

Issue - State: open - Opened by dollinad about 5 years ago

#46 - Gemini 5.2.10.49 crashes

Issue - State: open - Opened by Varunachander about 5 years ago

#46 - Gemini 5.2.10.49 crashes

Issue - State: open - Opened by Varunachander about 5 years ago

#45 - GeminiMulti_5.2.11.163 crashes

Issue - State: open - Opened by hansenaw over 5 years ago - 1 comment

#45 - GeminiMulti_5.2.11.163 crashes

Issue - State: open - Opened by hansenaw over 5 years ago - 1 comment

#44 - DP is greater than AD

Issue - State: open - Opened by roselucia over 5 years ago - 13 comments

#44 - DP is greater than AD

Issue - State: open - Opened by roselucia over 5 years ago - 13 comments

#43 - 1

Issue - State: closed - Opened by argoat over 5 years ago

#43 - 1

Issue - State: closed - Opened by argoat over 5 years ago

#42 - 5.2.11.163 tarballs not in gzip format?

Issue - State: closed - Opened by hansenaw over 5 years ago - 3 comments

#42 - 5.2.11.163 tarballs not in gzip format?

Issue - State: closed - Opened by hansenaw over 5 years ago - 3 comments

#41 - PG tag in Gemini malformatted

Issue - State: open - Opened by gwennberry over 5 years ago - 1 comment

#41 - PG tag in Gemini malformatted

Issue - State: open - Opened by gwennberry over 5 years ago - 1 comment

#40 - Add insert size (IS) tag to stitched reads in Gemini

Issue - State: open - Opened by gwennberry over 5 years ago

#40 - Add insert size (IS) tag to stitched reads in Gemini

Issue - State: open - Opened by gwennberry over 5 years ago

#39 - RMxN filter

Issue - State: closed - Opened by saty89 over 5 years ago - 3 comments

#39 - RMxN filter

Issue - State: closed - Opened by saty89 over 5 years ago - 3 comments

#38 - Error Gemini 5.2.11

Issue - State: open - Opened by XavierMialhe over 5 years ago - 8 comments

#38 - Error Gemini 5.2.11

Issue - State: open - Opened by XavierMialhe over 5 years ago - 8 comments

#37 - About the SNP result

Issue - State: open - Opened by hmyh1202 over 5 years ago - 1 comment

#37 - About the SNP result

Issue - State: open - Opened by hmyh1202 over 5 years ago - 1 comment

#36 - Release/pisces 5 2 11 open

Pull Request - State: closed - Opened by gwennberry over 5 years ago - 2 comments

#36 - Release/pisces 5 2 11 open

Pull Request - State: closed - Opened by gwennberry over 5 years ago - 2 comments

#35 - 5.2.11 release

Pull Request - State: closed - Opened by gwennberry over 5 years ago - 1 comment

#35 - 5.2.11 release

Pull Request - State: closed - Opened by gwennberry over 5 years ago - 1 comment

#34 - Pisces does not support multi-Mapped reads

Issue - State: open - Opened by chadisaad over 5 years ago - 3 comments

#34 - Pisces does not support multi-Mapped reads

Issue - State: open - Opened by chadisaad over 5 years ago - 3 comments

#33 - Gemini error - v5.2.10.49

Issue - State: open - Opened by saty89 over 5 years ago - 5 comments

#33 - Gemini error - v5.2.10.49

Issue - State: open - Opened by saty89 over 5 years ago - 5 comments

#32 - Pisces calling error - v5.2.10.49

Issue - State: open - Opened by saty89 over 5 years ago - 8 comments

#32 - Pisces calling error - v5.2.10.49

Issue - State: open - Opened by saty89 over 5 years ago - 8 comments

GitHub / illumina/pisces issues and pull requests