brentp / peddy

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

brentp/peddy Issues

gVCF input
Updated 3 months ago1
Running Ancestry Analysis on Samples with no Hets Found
Updated 6 months ago4
Inconsistent ancestry prediction of a sample using peddy on a cohort VCF and individual VCF
Closed a year ago2
KeyError in PCA.py
Closed a year ago8
Ancestry composition
Updated 2 years ago1
custom sites
Updated 2 years ago3
Validity of projected PC in peddy for covariate use
Closed 2 years ago1
Parallel processing blocked
Updated 2 years ago1
samples in vcf not in ped
Closed 2 years ago3
Runtime for large datasets.
Updated 3 years ago4
peddy sex-check incorrect prediction
Closed 3 years ago7
Error during pip install peddy
Closed 3 years ago2
No Hets found on numerous samples
Closed 6 years ago4
Question about idr_baf
Closed 4 years ago5
missing information in .peddy.ped
Closed 5 years ago5
Report which variants were used?
Updated 4 years ago1
How many Snps used in the PCA ?
Closed 4 years ago1
KeyError: 'keep' in peddy
Closed 4 years ago12
PCA projection - strange population classification
Updated 4 years ago3
Matplotlib issue? 'c' argument looks like a single numeric RGB or RGBA sequence
Closed 4 years ago4
Peddy run error: AttributeError: 'DataFrame' object has no attribute 'ix'
Updated 4 years ago2
IndexError: arrays used as indices must be of integer (or boolean) type
Closed 4 years ago7
Python version and libraries version incompatibility due to drop support for python 2.7
Updated 5 years ago2
can ped_check file differentiate parent-child versus sibling pairs?
Closed 5 years ago6
error loading tabix index
Closed 5 years ago5
Conda not found when building docker image for Peddy
Closed 5 years ago4
Library not loaded: @rpath/libdeflate.so
Updated 5 years ago1
mean depth is OK, but median depth is -2 for all sample
Closed 5 years ago3
Is Grch38 with chr prefix supported
Closed 5 years ago1
incorrect expected relatedness for consanguineous family
Updated 5 years ago6
Peddy error - RuntimeWarning
Updated 5 years ago
AttributeError: 'list' object has no attribute 'mom'
Closed 5 years ago
the performance of peddy in a vcf calling from exome sequencing
Updated 5 years ago1
Running Peddy with Single-cell vcf and ped file
Closed 5 years ago2
ped file "missing phenotype"
Updated 5 years ago1
report 1kg sample names in json output.
Updated 5 years ago
Explicitly enter duplicates in pedigree.
Updated 6 years ago1
Running peddy with provided vcf and ped file
Updated 6 years ago
peddy warning sampleID with leading zero
Closed 6 years ago2
Input PED file; replace sep with whitespace
Closed 6 years ago2
--Loglevel setting doesn't seem to work
Updated 6 years ago
Perform only ancestry-determination for sinlge sample
Closed 6 years ago2
pca sklearn failure in latest development version
Updated 6 years ago10
sex UNKNOWN
Updated 6 years ago1
support VCFs with only genotypes
Closed 6 years ago
process was killed, Memory Error.
Closed 6 years ago4
IndexError: list index out of range
Updated 6 years ago5
ped_check error -> ZeroDivisionError: float division
Closed 7 years ago3
IndexError: list index out of range (ped file is tab seperated and matplotlib is also updated).
Closed 7 years ago4
Sex check error
Closed 7 years ago2