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Answer: Answer: Generating .bed file and .map file for polyploid vcf file through plink
4 days ago by chrchang523 10k
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333
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Answer: Answer: Force PLINK2 to neglect chrX as the sex chromosome
13 days ago by chrchang523 10k
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379
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Answer: Answer: Easy way to find out which allele is minor allele from bed file?
13 days ago by chrchang523 10k
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446
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Answer: Answer: PCA results from PLINK and Hail vastly different
12 weeks ago by chrchang523 10k
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1
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538
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Answer: Answer: allele matching between identical genotypes
3 months ago by chrchang523 10k
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394
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Answer: Answer: number of homozygotes with phenotype
4 months ago by chrchang523 10k
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551
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Answer: Answer: HWE test different result according Pheno data
4 months ago by chrchang523 10k
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1
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477
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Answer: Answer: Clumping with r2=0 and 250kb radius in plink
6 months ago by chrchang523 10k
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505
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Answer: Answer: Plink Error
6 months ago by chrchang523 10k
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886
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Answer: Answer: Allele frequncies in plink including physical position in the output
7 months ago by chrchang523 10k
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1.2k
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Answer: Answer: Is there a way to get a list of all homogygous sites for each sample with plink
7 months ago by chrchang523 10k
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592
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Answer: Answer: Filter VCF File by VCF Format Variants
8 months ago by chrchang523 10k
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687
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Answer: Answer: reading pgen file into R
8 months ago by chrchang523 10k
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1.3k
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Answer: Answer: PLINK linear association testing command with an interaction and 2 covariates te
9 months ago by chrchang523 10k
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610
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Answer: Answer: Using -r2 in plink1.9 with .bim file that has CHR:POS entries
9 months ago by chrchang523 10k
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461
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Answer: Answer: VCFTools MAF Filter needs Efficiency Inquiry
9 months ago by chrchang523 10k
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500
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Answer: Answer: Assistance Needed with Converting VCF File for BOLT-LMM Usage
9 months ago by chrchang523 10k
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911
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Answer: Answer: PLINK1.9 check sex problem
10 months ago by chrchang523 10k
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612
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Answer: Answer: PLINK, Unphased heterozygous hardcalls in partially-phased variants are poorly r
11 months ago by chrchang523 10k
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0
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665
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Answer: Answer: Base-10 log transformed P-values and clump with plink v.1.9
11 months ago by chrchang523 10k
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465
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Answer: Answer: How do I restrict to only hm3 SNPs for plink analyses?
11 months ago by chrchang523 10k
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1.2k
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Answer: Answer: Linkage Disequilibrium with Plink
12 months ago by chrchang523 10k
2
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2.1k
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Answer: Answer: KING kinship inference error
12 months ago by chrchang523 10k
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754
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Answer: Answer: Where do I get a large reference VCF?
12 months ago by chrchang523 10k
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902
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Answer: Answer: PLINK Error: Invalid QUAL value on line
13 months ago by chrchang523 10k
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759
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Answer: Answer: Calculate the kinship matrix from NGS data
13 months ago by chrchang523 10k
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462
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Answer: Answer: invalid --hwe parameter sequence error when doing QC
15 months ago by chrchang523 10k
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0
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1.1k
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Answer: Answer: make BED file from existing BIM and FAM files
15 months ago by chrchang523 10k
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2.5k
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Answer: Answer: VCF to Plink files
15 months ago by chrchang523 10k
2
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1
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787
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Answer: Answer: drop duplicate insertion deletions in VCF at same position while keeping one
15 months ago by chrchang523 10k
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4.1k
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Answer: Answer: PLINK --geno and --mind
updated 16 months ago by 43k • written 16 months ago by 10k
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1.3k
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Answer: Answer: How to correct the long variants ID error?
16 months ago by chrchang523 10k
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1.3k
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Answer: Answer: How to measure pairwise genetic distance in all samples of a VCF file
18 months ago by chrchang523 10k
4
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2
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1.3k
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Answer: Answer: long view SNPs in vcf file
18 months ago by chrchang523 10k
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0
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612
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Answer: Answer: Calculate missing genotypes per sample with plink2
18 months ago by chrchang523 10k
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0
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1.7k
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Answer: Answer: PLINK1.9 Segmentation fault (core dumped)
18 months ago by chrchang523 10k
2
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2
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1.3k
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Answer: Answer: PLINK p value returning NA
19 months ago by chrchang523 10k
2
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0
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815
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Answer: Answer: Better splitting of mutliallelic sites then bcftools norm --m-any
20 months ago by chrchang523 10k
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1
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871
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Answer: Answer: plink2 fails to calculate allele frequency
20 months ago by chrchang523 10k
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1
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985
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Answer: Answer: Using a phenotype file with several phenotype columns- PLINK2
21 months ago by chrchang523 10k
3
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1
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1.4k
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Answer: Answer: SNP array plink to VCF validation issue
21 months ago by chrchang523 10k
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2
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2.3k
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Answer: Answer: Plink : Variant names are limited to 16000 characters
21 months ago by chrchang523 10k
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1
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2.2k
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Answer: Answer: High proportion of non-biallelic SNPs in dbSNP 155 vs 144
21 months ago by chrchang523 10k
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1
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2.9k
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Answer: Answer: set-all-var-ids misuse in plink 2.0
21 months ago by chrchang523 10k
2
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2
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1.1k
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Answer: Answer: Changing from "rs" to "chr_pos_ref_alt"
21 months ago by chrchang523 10k
2
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1
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649
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Answer: Answer: PRS with multiple panels of SNP weights
21 months ago by chrchang523 10k
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1
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1.3k
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Answer: Answer: updating .bim with new rsids
22 months ago by chrchang523 10k
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1
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672
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Answer: Answer: plink update .bim question
22 months ago by chrchang523 10k
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1
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796
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Answer: Answer: How can I keep INFO value when convert bgen to VCF by using plink2?
22 months ago by chrchang523 10k
2
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1
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929
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Answer: Answer: Plink runtime when using "--extract"
23 months ago by chrchang523 10k
442 results • Page 1 of 9
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