Ecosyste.ms: Issues

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GitHub / brentp/peddy issues and pull requests

#91 - gVCF input

Issue - State: open - Opened by zoeward-nz 6 months ago - 1 comment

#89 - Ancestry composition

Issue - State: open - Opened by RoniHaas almost 2 years ago - 1 comment

#88 - custom sites

Issue - State: open - Opened by cartographerJ about 2 years ago - 3 comments

#87 - Validity of projected PC in peddy for covariate use

Issue - State: closed - Opened by Dzhan4 over 2 years ago - 1 comment

#86 - Parallel processing blocked

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

#85 - samples in vcf not in ped

Issue - State: closed - Opened by Giuseppe1995 over 2 years ago - 3 comments

#84 - Runtime for large datasets.

Issue - State: open - Opened by sdsilva10 about 3 years ago - 4 comments

#83 - Error during pip install peddy

Issue - State: closed - Opened by lyj95618 over 3 years ago - 2 comments

#82 - Question about idr_baf

Issue - State: closed - Opened by mingoo426 almost 4 years ago - 5 comments

#81 - Report which variants were used?

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

#80 - How many Snps used in the PCA ?

Issue - State: closed - Opened by ymavura3 about 4 years ago - 1 comment

#79 - KeyError: 'keep' in peddy

Issue - State: closed - Opened by liu7923 over 4 years ago - 12 comments

#78 - PCA projection - strange population classification

Issue - State: open - Opened by numicator over 4 years ago - 3 comments

#76 - Peddy run error: AttributeError: 'DataFrame' object has no attribute 'ix'

Issue - State: open - Opened by yusmile0618 over 4 years ago - 2 comments

#75 - IndexError: arrays used as indices must be of integer (or boolean) type

Issue - State: closed - Opened by numicator over 4 years ago - 7 comments

#74 - peddy sex-check incorrect prediction

Issue - State: closed - Opened by Fazulur over 4 years ago - 7 comments

#73 - can ped_check file differentiate parent-child versus sibling pairs?

Issue - State: closed - Opened by wangfan860 almost 5 years ago - 6 comments

#72 - error loading tabix index

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

#71 - missing information in .peddy.ped

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

#69 - Running Ancestry Analysis on Samples with no Hets Found

Issue - State: open - Opened by angelussong about 5 years ago - 4 comments

#68 - Conda not found when building docker image for Peddy

Issue - State: closed - Opened by claudiadast about 5 years ago - 4 comments

#67 - Is Grch38 with chr prefix supported

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

#66 - mean depth is OK, but median depth is -2 for all sample

Issue - State: closed - Opened by wym0072003 about 5 years ago - 3 comments

#65 - Peddy error - RuntimeWarning

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

#64 - Library not loaded: @rpath/libdeflate.so

Issue - State: open - Opened by maksjutov about 5 years ago - 1 comment

#63 - AttributeError: 'list' object has no attribute 'mom'

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

#62 - the performance of peddy in a vcf calling from exome sequencing

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

#61 - Running Peddy with Single-cell vcf and ped file

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

#59 - add requirements to setup.py

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

#58 - ped file "missing phenotype"

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

#57 - report 1kg sample names in json output.

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

#56 - incorrect expected relatedness for consanguineous family

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

#55 - Explicitly enter duplicates in pedigree.

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

#54 - Running peddy with provided vcf and ped file

Issue - State: open - Opened by julien-kann almost 6 years ago

#53 - Fix vcf filename in README.md

Pull Request - State: closed - Opened by splichte almost 6 years ago - 1 comment

#52 - peddy warning sampleID with leading zero

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

#51 - Input PED file; replace sep with whitespace

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

#50 - No Hets found on numerous samples

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

#49 - --Loglevel setting doesn't seem to work

Issue - State: open - Opened by vivianTan7 over 6 years ago

#48 - KeyError in PCA.py

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

#47 - Perform only ancestry-determination for sinlge sample

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

#46 - Broken

Pull Request - State: closed - Opened by brentp over 6 years ago

#45 - pca sklearn failure in latest development version

Issue - State: open - Opened by chapmanb over 6 years ago - 10 comments

#44 - Easier specification of build 38/build 37 sites

Pull Request - State: closed - Opened by chapmanb over 6 years ago - 3 comments

#43 - sex UNKNOWN

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

#42 - Modified sites with compatibility for GRCH38 (hg38)

Pull Request - State: closed - Opened by mikecormier over 6 years ago - 2 comments

#41 - support VCFs with only genotypes

Issue - State: closed - Opened by brentp over 6 years ago
Labels: enhancement

#40 - process was killed, Memory Error.

Issue - State: closed - Opened by wym0072003 over 6 years ago - 4 comments

#39 - IndexError: list index out of range

Issue - State: open - Opened by UmerMaqsood10 over 6 years ago - 5 comments

#38 - Liftover

Pull Request - State: closed - Opened by mikecormier almost 7 years ago

#37 - ped_check error -> ZeroDivisionError: float division

Issue - State: closed - Opened by yocra3 almost 7 years ago - 3 comments

#36 - Sex check error

Issue - State: closed - Opened by nskbe almost 7 years ago - 2 comments

#34 - Adapt to networkx >=2.0 which dropped *_iter() methods.

Pull Request - State: closed - Opened by cbrueffer about 7 years ago - 1 comment

#33 - support for hg38 and single chromosome

Issue - State: closed - Opened by joonan30 about 7 years ago - 18 comments

#32 - question about PCA plot

Issue - State: closed - Opened by liushuangmms about 7 years ago - 1 comment

#31 - get warning when run peddy

Issue - State: open - Opened by liushuangmms about 7 years ago - 12 comments

#30 - Peddy version in output

Issue - State: closed - Opened by henrikstranneheim over 7 years ago - 3 comments

#29 - X server dependency error

Issue - State: closed - Opened by henrikstranneheim over 7 years ago - 15 comments

#28 - Problem with pandas and python 3

Issue - State: closed - Opened by moonso over 7 years ago - 6 comments

#27 - Updates CLI and adds logging

Pull Request - State: closed - Opened by moonso over 7 years ago - 7 comments

#26 - output kinship file?

Issue - State: closed - Opened by jxchong over 7 years ago - 1 comment

#25 - ouput contamination estimate

Issue - State: open - Opened by brentp over 7 years ago - 1 comment

#24 - Only plot PCA from cohort without doing any other analysis

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

#23 - Python/CyVCF2 error: "ZeroDivisionError: float division"

Issue - State: closed - Opened by robinandeer over 7 years ago - 11 comments

#22 - can you use `https://cdn.plot.ly/plotly-latest.min.js` for plotly

Issue - State: closed - Opened by leipzig almost 8 years ago - 1 comment

#21 - Half-siblings are treated as full siblings

Issue - State: open - Opened by oleraj almost 8 years ago - 7 comments
Labels: bug

#20 - 1000 genomes PCA data

Issue - State: closed - Opened by ewels almost 8 years ago - 12 comments

#19 - Use https for plotly-latest.min.js

Pull Request - State: closed - Opened by cassimons about 8 years ago - 1 comment

#18 - IndexError: list index out of range

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

#17 - allow lasso selection of points to get unrelated (or whichever) samples

Issue - State: open - Opened by brentp about 8 years ago - 1 comment

#16 - allow exporting HTML table to csv

Issue - State: closed - Opened by brentp about 8 years ago

#15 - handle 'chr' prefix

Issue - State: closed - Opened by brentp about 8 years ago - 3 comments

#14 - check Y chromosome

Issue - State: open - Opened by brentp over 8 years ago - 2 comments

#13 - add per-sample call-rate to vis

Issue - State: closed - Opened by brentp over 8 years ago - 1 comment

#12 - add jitter to sex-check plot for html

Issue - State: closed - Opened by brentp over 8 years ago

#11 - interactive plots

Issue - State: closed - Opened by brentp over 8 years ago - 3 comments

#10 - size points by number of good calls

Issue - State: closed - Opened by brentp over 8 years ago

#9 - missing samples

Issue - State: closed - Opened by brentp over 8 years ago

#8 - PCA

Issue - State: closed - Opened by brentp over 8 years ago

#7 - qc by family

Issue - State: closed - Opened by brentp almost 9 years ago

#6 - heterozygosity

Issue - State: closed - Opened by brentp almost 9 years ago - 1 comment

#5 - use linkage blocks

Issue - State: closed - Opened by brentp about 9 years ago

#4 - QC tutorial

Issue - State: closed - Opened by brentp about 9 years ago

#3 - Why isn't this project called pedagree?

Issue - State: closed - Opened by arq5x about 9 years ago - 3 comments

#2 - pip install fails to find `__version__` string

Issue - State: closed - Opened by mdshw5 over 9 years ago - 3 comments

#1 - Support for specific families.

Issue - State: closed - Opened by arq5x over 9 years ago - 1 comment