brentp/somalier issues and pull requests

#100 - Matching Called VCF and Uncalled CRAMs

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

#100 - Matching Called VCF and Uncalled CRAMs

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

#99 - Filtering on nsites

Issue - State: open - Opened by marcustutert over 2 years ago - 5 comments

#99 - Filtering on nsites

Issue - State: open - Opened by marcustutert over 2 years ago - 5 comments

#98 - Error extracting from a VCF

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

#98 - Error extracting from a VCF

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

#97 - merging somalier files for different chromosomes

Issue - State: closed - Opened by burakalver over 2 years ago - 4 comments

#97 - merging somalier files for different chromosomes

Issue - State: closed - Opened by burakalver over 2 years ago - 4 comments

#96 - Error with find-sites

Issue - State: open - Opened by ashotmarg over 2 years ago - 15 comments

#96 - Error with find-sites

Issue - State: open - Opened by ashotmarg over 2 years ago - 15 comments

#95 - Increasing Number of SNPs improving inference?

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

#95 - Increasing Number of SNPs improving inference?

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

#94 - No output - docker

Issue - State: closed - Opened by krukanna over 2 years ago - 4 comments

#94 - No output - docker

Issue - State: closed - Opened by krukanna over 2 years ago - 4 comments

#93 - somalier ancestry and relate freeze on writing output on BeeGFS filesystem

Issue - State: open - Opened by edg1983 over 2 years ago - 5 comments

#93 - somalier ancestry and relate freeze on writing output on BeeGFS filesystem

Issue - State: open - Opened by edg1983 over 2 years ago - 5 comments

#92 - Bioconda recipe for somalier

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

#92 - Bioconda recipe for somalier

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

#91 - known mouse sites

Issue - State: open - Opened by igordot over 2 years ago - 5 comments

#91 - known mouse sites

Issue - State: open - Opened by igordot over 2 years ago - 5 comments

#90 - Sample id duplicates

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

#90 - Sample id duplicates

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

#89 - Runtime with large datasets

Issue - State: open - Opened by marcustutert almost 3 years ago - 39 comments

#89 - Runtime with large datasets

Issue - State: open - Opened by marcustutert almost 3 years ago - 39 comments

#88 - Found Zero Sites

Issue - State: open - Opened by marcustutert almost 3 years ago - 9 comments

#88 - Found Zero Sites

Issue - State: open - Opened by marcustutert almost 3 years ago - 9 comments

#87 - Licensing

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

#87 - Licensing

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

#86 - n in relatedness result

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

#86 - n in relatedness result

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

#85 - Update README.md to include cmd descriptions

Pull Request - State: closed - Opened by zztin almost 3 years ago - 2 comments

#85 - Update README.md to include cmd descriptions

Pull Request - State: closed - Opened by zztin almost 3 years ago - 2 comments

#84 - Update relate.nim for better formatting

Pull Request - State: closed - Opened by zztin almost 3 years ago - 1 comment

#84 - Update relate.nim for better formatting

Pull Request - State: closed - Opened by zztin almost 3 years ago - 1 comment

#83 - HTML report

Issue - State: closed - Opened by Danisov almost 3 years ago - 5 comments

#83 - HTML report

Issue - State: closed - Opened by Danisov almost 3 years ago - 5 comments

#82 - Issue extracting variants with VCF

Issue - State: closed - Opened by holtjma almost 3 years ago - 5 comments

#82 - Issue extracting variants with VCF

Issue - State: closed - Opened by holtjma almost 3 years ago - 5 comments

#81 - somalier ancestry : Argument list too long

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

#81 - somalier ancestry : Argument list too long

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

#80 - Comparing Results with Multiple Samples with Same Name

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

#80 - Comparing Results with Multiple Samples with Same Name

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

#79 - Checking concordance between RNA and DNA samples

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

#79 - Checking concordance between RNA and DNA samples

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

#78 - relatedness results question

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

#78 - relatedness results question

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

#77 - SIGSEGV error for somalier ancestry

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

#77 - SIGSEGV error for somalier ancestry

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

#76 - missing pairs - somalier relate v. >= 0.2.7

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

#76 - missing pairs - somalier relate v. >= 0.2.7

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

#75 - minimum number of sites

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

#75 - minimum number of sites

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

#74 - Definition of relatedness as implemented in somalier

Issue - State: open - Opened by asp8200 over 3 years ago - 1 comment

#74 - Definition of relatedness as implemented in somalier

Issue - State: open - Opened by asp8200 over 3 years ago - 1 comment

#73 - Sex QC

Issue - State: closed - Opened by jrejente over 3 years ago - 9 comments

#73 - Sex QC

Issue - State: closed - Opened by jrejente over 3 years ago - 9 comments

#72 - Running somalier on bam files in s3?

Issue - State: open - Opened by nspies-celsiustx over 3 years ago - 3 comments

#72 - Running somalier on bam files in s3?

Issue - State: open - Opened by nspies-celsiustx over 3 years ago - 3 comments

#71 - Issue with reading mutect2 output on somalier (fileformat=VCFv4.2)

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

#71 - Issue with reading mutect2 output on somalier (fileformat=VCFv4.2)

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

#70 - Feature request: install somalier from anaconda

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

#70 - Feature request: install somalier from anaconda

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

#69 - How to specify tumor/normal pairs

Issue - State: closed - Opened by V-Catherine almost 4 years ago - 9 comments

#69 - How to specify tumor/normal pairs

Issue - State: closed - Opened by V-Catherine almost 4 years ago - 9 comments

#68 - Static OSX binary?

Issue - State: open - Opened by ssadedin almost 4 years ago - 6 comments

#68 - Static OSX binary?

Issue - State: open - Opened by ssadedin almost 4 years ago - 6 comments

#67 - Ancestry estimate using gnomad v3 data?

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

#67 - Ancestry estimate using gnomad v3 data?

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

#66 - ancestry output error

Issue - State: closed - Opened by olenamarchenko1234 almost 4 years ago - 6 comments

#66 - ancestry output error

Issue - State: closed - Opened by olenamarchenko1234 almost 4 years ago - 6 comments

#65 - ENH: add read_haps algorithm to estimate contamination

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

#65 - ENH: add read_haps algorithm to estimate contamination

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

#64 - any plans to bring back the option to use multiple threads?

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

#64 - any plans to bring back the option to use multiple threads?

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

#63 - Comparison 1 to n samples

Issue - State: open - Opened by svural about 4 years ago

#63 - Comparison 1 to n samples

Issue - State: open - Opened by svural about 4 years ago

#62 - full results from relate output

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

#62 - full results from relate output

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

#61 - Runtime for ancestry estimate?

Issue - State: open - Opened by bhanratt about 4 years ago - 9 comments

#61 - Runtime for ancestry estimate?

Issue - State: open - Opened by bhanratt about 4 years ago - 9 comments

#60 - Generated html file empty

Issue - State: open - Opened by dBenedek about 4 years ago - 9 comments

#60 - Generated html file empty

Issue - State: open - Opened by dBenedek about 4 years ago - 9 comments

#59 - Ancestry Error: unhandled exception: couldn't open sketch file

Issue - State: closed - Opened by bopohdr about 4 years ago - 7 comments

#59 - Ancestry Error: unhandled exception: couldn't open sketch file

Issue - State: closed - Opened by bopohdr about 4 years ago - 7 comments

#58 - High relatedness for many unrelated individuals

Issue - State: closed - Opened by lindenb over 4 years ago - 5 comments

#58 - High relatedness for many unrelated individuals

Issue - State: closed - Opened by lindenb over 4 years ago - 5 comments

#57 - headers for unprefixed genome builds have chr prefix

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

#57 - headers for unprefixed genome builds have chr prefix

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

#56 - Allow to specify homozygote call threashold

Issue - State: closed - Opened by fgvieira over 4 years ago

#56 - Allow to specify homozygote call threashold

Issue - State: closed - Opened by fgvieira over 4 years ago

#55 - Somalier underestimates relatedness if low sites overlap

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

#55 - Somalier underestimates relatedness if low sites overlap

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

#54 - Missing relatedness pair

Issue - State: closed - Opened by eyu8 over 4 years ago - 2 comments

#54 - Missing relatedness pair

Issue - State: closed - Opened by eyu8 over 4 years ago - 2 comments

#53 - Illegals storage access. (Attempt to read from nil)

Issue - State: closed - Opened by vdejager over 4 years ago - 6 comments

#53 - Illegals storage access. (Attempt to read from nil)

Issue - State: closed - Opened by vdejager over 4 years ago - 6 comments

#52 - Docker v0.2.10 missing

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

#52 - Docker v0.2.10 missing

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

#51 - Basic IBSX question

Issue - State: closed - Opened by holtjma over 4 years ago - 5 comments

#51 - Basic IBSX question

Issue - State: closed - Opened by holtjma over 4 years ago - 5 comments

GitHub / brentp/somalier issues and pull requests