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Dear Christopher,
I was looking at the IBS calculations produced by plink 1.9, and observed some problems relevant to my work. I created a minimal BED file with just one SNP and with 4 individuals…
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Original bug report at https://groups.google.com/g/plink2-users/c/ABcn9tN6ttA .
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The pipeline looks like it is optimized for processing imputed vcf data from UMICH or TOPMed imputation server which generates a DS field. Is is possible to run the pipeline on GATK WGS sequencing …
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Implement algorithm for RT Relationship type inferred from .fam/.ped file
RT est un champ du fichier produit par la commande --genome
https://www.cog-genomics.org/plink2/ibd
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After updating from 2.3.8 to 2.3.9 I can not get pLink2 to work off raw files. The same protocol as before, no changes to set up other than updated pLink. It starts and then hangs on for 60+ min at th…
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In round tripping vcf- > pgen(pvar/psam) -> vcf, contig names are not preserved:
Original VCF (one contig named "chr1"):
```
##fileformat=VCFv4.2
##contig=
#CHROM POS ID REF AL…
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Hi,
I tried pLink2 and followed the instruction to add a new crosslinker but after hitting save, the pconfig window just disappear and I didn't see any linker added.
Thanks,
Duc
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Hello,
I have pulled out the T1D GRS1 snps from genotype data stored in .bgen files and converted them to a vcf 4.2 file using plink2 which I think should be compatible with diabetesRiskScores:
…
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Figure 3: Imputation Filters compared
A.
Imputation Schematic using plink2/SHAPEIT then Joining; only use SNPs
remove NA12878 pedigree variants from the imputation reference file
B.
F…
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reprosteps: download prerequisites as described in http://localhost:8891/notebooks/gwas101.ipynb, then execute
```import os
from gwas_tools import read_bed, write_bed
os.system('plink2 --bfile chr2…