brentp peddy issues - Githubissues

brentp / peddy

genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF

MIT License

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issues

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gVCF input

#91 zoeward-nz opened 5 months ago
1
Inconsistent ancestry prediction of a sample using peddy on a cohort VCF and individual VCF

#90 anjalijain22 closed 1 year ago
2
Ancestry composition

#89 RoniHaas opened 1 year ago
1
custom sites

#88 cartographerJ opened 2 years ago
3
Validity of projected PC in peddy for covariate use

#87 Dzhan4 closed 2 years ago
1
Parallel processing blocked

#86 MattWellie opened 2 years ago
1
samples in vcf not in ped

#85 Giuseppe1995 closed 2 years ago
3
Runtime for large datasets.

#84 sdsilva10 opened 3 years ago
4
Error during pip install peddy

#83 lyj95618 closed 3 years ago
2
Question about idr_baf

#82 mingoo426 closed 3 years ago
5
Report which variants were used?

#81 bhanratt opened 4 years ago
1
How many Snps used in the PCA ?

#80 ymavura3 closed 4 years ago
1
KeyError: 'keep' in peddy

#79 liu7923 closed 4 years ago
12
PCA projection - strange population classification

#78 numicator opened 4 years ago
3
Matplotlib issue? 'c' argument looks like a single numeric RGB or RGBA sequence

#77 julieefeusier closed 4 years ago
4
Peddy run error: AttributeError: 'DataFrame' object has no attribute 'ix'

#76 yusmile0618 opened 4 years ago
2
IndexError: arrays used as indices must be of integer (or boolean) type

#75 numicator closed 4 years ago
7
peddy sex-check incorrect prediction

#74 Fazulur closed 3 years ago
7
can ped_check file differentiate parent-child versus sibling pairs?

#73 wangfan860 closed 4 years ago
6
error loading tabix index

#72 ccymak closed 4 years ago
5
missing information in .peddy.ped

#71 olneykimberly closed 4 years ago
5
Python version and libraries version incompatibility due to drop support for python 2.7

#70 NikolaBio opened 5 years ago
2
Running Ancestry Analysis on Samples with no Hets Found

#69 angelussong opened 5 years ago
4
Conda not found when building docker image for Peddy

#68 claudiadast closed 5 years ago
4
Is Grch38 with chr prefix supported

#67 henrikstranneheim closed 5 years ago
1
mean depth is OK, but median depth is -2 for all sample

#66 wym0072003 closed 5 years ago
3
Peddy error - RuntimeWarning

#65 evagradovich opened 5 years ago
0
Library not loaded: @rpath/libdeflate.so

#64 maksjutov opened 5 years ago
1
AttributeError: 'list' object has no attribute 'mom'

#63 claudiadast closed 5 years ago
0
the performance of peddy in a vcf calling from exome sequencing

#62 N-damo opened 5 years ago
1
Running Peddy with Single-cell vcf and ped file

#61 angelussong closed 5 years ago
2
add requirements to setup.py

#59 sndrtj closed 5 years ago
1
ped file "missing phenotype"

#58 svergult opened 5 years ago
1
report 1kg sample names in json output.

#57 brentp opened 5 years ago
0
incorrect expected relatedness for consanguineous family

#56 ekarlins opened 5 years ago
6
Explicitly enter duplicates in pedigree.

#55 OgnjenMilicevic opened 5 years ago
1
Running peddy with provided vcf and ped file

#54 julien-kann opened 5 years ago
0
Fix vcf filename in README.md

#53 splichte closed 5 years ago
1
peddy warning sampleID with leading zero

#52 Fazulur closed 5 years ago
2
Input PED file; replace sep with whitespace

#51 jrouhana closed 5 years ago
2
No Hets found on numerous samples

#50 AndrewSkelton closed 6 years ago
4
--Loglevel setting doesn't seem to work

#49 vivianTan7 opened 6 years ago
0
KeyError in PCA.py

#48 skgttjo closed 1 year ago
8
Perform only ancestry-determination for sinlge sample

#47 imgag closed 6 years ago
2
Broken

#46 brentp closed 6 years ago
0
pca sklearn failure in latest development version

#45 chapmanb opened 6 years ago
10
Easier specification of build 38/build 37 sites

#44 chapmanb closed 6 years ago
3
sex UNKNOWN

#43 jeffverboon opened 6 years ago
1
Modified sites with compatibility for GRCH38 (hg38)

#42 mikecormier closed 6 years ago
2
support VCFs with only genotypes

#41 brentp closed 6 years ago
0