Ecosyste.ms: Issues

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GitHub / brentp/somalier issues and pull requests

#49 - add option to scale ibs0 and ibs2 by n

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

#49 - add option to scale ibs0 and ibs2 by n

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

#48 - meaning of warning:cant use more than 65535 sites

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

#48 - meaning of warning:cant use more than 65535 sites

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

#47 - wrong header on relate pairs output

Issue - State: closed - Opened by fgvieira over 4 years ago - 1 comment

#47 - wrong header on relate pairs output

Issue - State: closed - Opened by fgvieira over 4 years ago - 1 comment

#46 - Crash with 0.2.9

Issue - State: closed - Opened by holtjma over 4 years ago - 8 comments

#46 - Crash with 0.2.9

Issue - State: closed - Opened by holtjma over 4 years ago - 8 comments

#45 - Limit number of threads used

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

#45 - Limit number of threads used

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

#43 - Distinguish between bam files having the same bam sample ID

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

#43 - Distinguish between bam files having the same bam sample ID

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

#42 - show warning when .somalier files have no sites with depth > 0

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

#42 - show warning when .somalier files have no sites with depth > 0

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

#41 - Added option to prefix sample names in the digests

Pull Request - State: closed - Opened by kpalin over 4 years ago - 4 comments

#41 - Added option to prefix sample names in the digests

Pull Request - State: closed - Opened by kpalin over 4 years ago - 4 comments

#40 - unspecified parent

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

#40 - unspecified parent

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

#39 - gVCF v. VCF outputs

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

#38 - html: hover in select-box should show short description

Issue - State: closed - Opened by brentp almost 5 years ago - 1 comment

#38 - html: hover in select-box should show short description

Issue - State: closed - Opened by brentp almost 5 years ago - 1 comment

#37 - `Argument list too long' on 30k samples

Issue - State: closed - Opened by asazonov almost 5 years ago - 2 comments

#37 - `Argument list too long' on 30k samples

Issue - State: closed - Opened by asazonov almost 5 years ago - 2 comments

#36 - Feature request: output per site info (e.g. genotype, depth)

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

#36 - Feature request: output per site info (e.g. genotype, depth)

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

#35 - ancestry

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

#35 - ancestry

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

#34 - Deep

Pull Request - State: closed - Opened by brentp about 5 years ago

#34 - Deep

Pull Request - State: closed - Opened by brentp about 5 years ago

#33 - Feature request: option to ignore filters

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

#33 - Feature request: option to ignore filters

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

#32 - subset unrelated samples for large cohorts

Issue - State: closed - Opened by brentp about 5 years ago - 1 comment

#32 - subset unrelated samples for large cohorts

Issue - State: closed - Opened by brentp about 5 years ago - 1 comment

#31 - `[somalier] found 0 sites' error when extracting from array .vcf.gz

Issue - State: closed - Opened by asazonov about 5 years ago - 31 comments

#31 - `[somalier] found 0 sites' error when extracting from array .vcf.gz

Issue - State: closed - Opened by asazonov about 5 years ago - 31 comments

#30 - IBD

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

#30 - IBD

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

#29 - Add groups

Pull Request - State: closed - Opened by brentp about 5 years ago

#29 - Add groups

Pull Request - State: closed - Opened by brentp about 5 years ago

#28 - Add principal component export for bg and sample in ancestry-predict.py

Pull Request - State: closed - Opened by tstannius about 5 years ago - 4 comments

#28 - Add principal component export for bg and sample in ancestry-predict.py

Pull Request - State: closed - Opened by tstannius about 5 years ago - 4 comments

#27 - Feature Request: Support gVCF

Issue - State: closed - Opened by holtjma about 5 years ago - 13 comments

#27 - Feature Request: Support gVCF

Issue - State: closed - Opened by holtjma about 5 years ago - 13 comments

#26 - Suggestion: use groups info (same individual) to infer expected relatedness

Issue - State: closed - Opened by fgvieira about 5 years ago - 5 comments

#26 - Suggestion: use groups info (same individual) to infer expected relatedness

Issue - State: closed - Opened by fgvieira about 5 years ago - 5 comments

#25 - Add plot option to ancestry-predict.py

Issue - State: closed - Opened by fgvieira about 5 years ago

#25 - Add plot option to ancestry-predict.py

Issue - State: closed - Opened by fgvieira about 5 years ago

#24 - `ancestry-predict.py` error

Issue - State: closed - Opened by fgvieira about 5 years ago - 2 comments

#24 - `ancestry-predict.py` error

Issue - State: closed - Opened by fgvieira about 5 years ago - 2 comments

#23 - correct for population structure in relatedness

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

#23 - correct for population structure in relatedness

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

#22 - release 0.2.1?

Issue - State: closed - Opened by brwnj over 5 years ago - 1 comment

#21 - Updates results.html

Pull Request - State: closed - Opened by brwnj over 5 years ago

#21 - Updates results.html

Pull Request - State: closed - Opened by brwnj over 5 years ago

#20 - Updates HTML

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

#20 - Updates HTML

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

#19 - new tool fam-finder

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

#19 - new tool fam-finder

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

#18 - unify markers for GRCh37, hg38

Issue - State: closed - Opened by brentp over 5 years ago - 1 comment

#18 - unify markers for GRCh37, hg38

Issue - State: closed - Opened by brentp over 5 years ago - 1 comment

#17 - add genomic depth view

Issue - State: closed - Opened by brentp over 5 years ago - 1 comment

#17 - add genomic depth view

Issue - State: closed - Opened by brentp over 5 years ago - 1 comment

#16 - Sub commands

Pull Request - State: closed - Opened by brentp over 5 years ago

#16 - Sub commands

Pull Request - State: closed - Opened by brentp over 5 years ago

#14 - Some grouped pairs in groups.csv shown as 'unrelated' in .html

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

#14 - Some grouped pairs in groups.csv shown as 'unrelated' in .html

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

#13 - nan values break output .html

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

#12 - ENH: diagnostic output of proportion of sites with AB not in [0.2, 0.8]

Issue - State: closed - Opened by brentp over 5 years ago - 1 comment

#11 - relatedness calculation

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

#10 - html: add box to enter sample name for highlighting.

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

#8 - cross individual contamination estimation

Issue - State: open - Opened by mflevine over 5 years ago - 36 comments

#7 - Large number of n_unknown

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

#6 - output % of split reads

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

#5 - relatedness = -nan and no HETs found

Issue - State: closed - Opened by lconde-ucl almost 6 years ago - 14 comments

#4 - Erroneous "index not found" errors

Issue - State: closed - Opened by jblachly almost 6 years ago - 12 comments

#3 - cancer ChIPseq data and whole exome data

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

#2 - site-selection with BS-Seq in mind

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

#1 - images

Issue - State: closed - Opened by brentp about 6 years ago