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0
votes
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replies
198
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Answer:
Answer: Generating .bed file and .map file for polyploid vcf file through plink
6 days ago by
chrchang523
10k
1
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0
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346
views
Answer:
Answer: Force PLINK2 to neglect chrX as the sex chromosome
15 days ago by
chrchang523
10k
0
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0
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401
views
Answer:
Answer: Easy way to find out which allele is minor allele from bed file?
15 days ago by
chrchang523
10k
1
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0
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452
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Answer:
Answer: PCA results from PLINK and Hail vastly different
12 weeks ago by
chrchang523
10k
0
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1
reply
541
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Answer:
Answer: allele matching between identical genotypes
3 months ago by
chrchang523
10k
2
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1
reply
399
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Answer:
Answer: number of homozygotes with phenotype
4 months ago by
chrchang523
10k
2
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1
reply
554
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Answer:
Answer: HWE test different result according Pheno data
4 months ago by
chrchang523
10k
1
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1
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484
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Answer:
Answer: Clumping with r2=0 and 250kb radius in plink
6 months ago by
chrchang523
10k
0
votes
0
replies
508
views
Answer:
Answer: Plink Error
6 months ago by
chrchang523
10k
0
votes
1
reply
891
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Answer:
Answer: Allele frequncies in plink including physical position in the output
7 months ago by
chrchang523
10k
0
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0
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1.2k
views
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
2
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0
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593
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Answer:
Answer: Filter VCF File by VCF Format Variants
8 months ago by
chrchang523
10k
3
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0
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690
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Answer:
Answer: reading pgen file into R
9 months ago by
chrchang523
10k
0
votes
1
reply
1.4k
views
Answer:
Answer: PLINK linear association testing command with an interaction and 2 covariates te
10 months ago by
chrchang523
10k
0
votes
0
replies
613
views
Answer:
Answer: Using -r2 in plink1.9 with .bim file that has CHR:POS entries
10 months ago by
chrchang523
10k
0
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0
replies
463
views
Answer:
Answer: VCFTools MAF Filter needs Efficiency Inquiry
10 months ago by
chrchang523
10k
0
votes
0
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502
views
Answer:
Answer: Assistance Needed with Converting VCF File for BOLT-LMM Usage
10 months ago by
chrchang523
10k
0
votes
0
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915
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Answer:
Answer: PLINK1.9 check sex problem
10 months ago by
chrchang523
10k
0
votes
0
replies
613
views
Answer:
Answer: PLINK, Unphased heterozygous hardcalls in partially-phased variants are poorly r
11 months ago by
chrchang523
10k
1
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0
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667
views
Answer:
Answer: Base-10 log transformed P-values and clump with plink v.1.9
11 months ago by
chrchang523
10k
1
vote
0
replies
469
views
Answer:
Answer: How do I restrict to only hm3 SNPs for plink analyses?
11 months ago by
chrchang523
10k
0
votes
1
reply
1.2k
views
Answer:
Answer: Linkage Disequilibrium with Plink
12 months ago by
chrchang523
10k
2
votes
0
replies
2.1k
views
Answer:
Answer: KING kinship inference error
12 months ago by
chrchang523
10k
1
vote
0
replies
755
views
Answer:
Answer: Where do I get a large reference VCF?
12 months ago by
chrchang523
10k
1
vote
1
reply
904
views
Answer:
Answer: PLINK Error: Invalid QUAL value on line
13 months ago by
chrchang523
10k
2
votes
0
replies
763
views
Answer:
Answer: Calculate the kinship matrix from NGS data
13 months ago by
chrchang523
10k
0
votes
0
replies
465
views
Answer:
Answer: invalid --hwe parameter sequence error when doing QC
15 months ago by
chrchang523
10k
0
votes
0
replies
1.1k
views
Answer:
Answer: make BED file from existing BIM and FAM files
15 months ago by
chrchang523
10k
1
vote
1
reply
2.5k
views
Answer:
Answer: VCF to Plink files
15 months ago by
chrchang523
10k
2
votes
1
reply
790
views
Answer:
Answer: drop duplicate insertion deletions in VCF at same position while keeping one
15 months ago by
chrchang523
10k
1
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1
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4.1k
views
Answer:
Answer: PLINK --geno and --mind
updated 16 months ago by
Ram
43k • written 16 months ago by
chrchang523
10k
1
vote
1
reply
1.3k
views
Answer:
Answer: How to correct the long variants ID error?
16 months ago by
chrchang523
10k
0
votes
0
replies
1.3k
views
Answer:
Answer: How to measure pairwise genetic distance in all samples of a VCF file
18 months ago by
chrchang523
10k
4
votes
2
replies
1.3k
views
Answer:
Answer: long view SNPs in vcf file
18 months ago by
chrchang523
10k
1
vote
0
replies
613
views
Answer:
Answer: Calculate missing genotypes per sample with plink2
18 months ago by
chrchang523
10k
0
votes
0
replies
1.7k
views
Answer:
Answer: PLINK1.9 Segmentation fault (core dumped)
18 months ago by
chrchang523
10k
2
votes
2
replies
1.3k
views
Answer:
Answer: PLINK p value returning NA
19 months ago by
chrchang523
10k
2
votes
0
replies
821
views
Answer:
Answer: Better splitting of mutliallelic sites then bcftools norm --m-any
20 months ago by
chrchang523
10k
0
votes
1
reply
872
views
Answer:
Answer: plink2 fails to calculate allele frequency
20 months ago by
chrchang523
10k
1
vote
1
reply
985
views
Answer:
Answer: Using a phenotype file with several phenotype columns- PLINK2
21 months ago by
chrchang523
10k
3
votes
1
reply
1.4k
views
Answer:
Answer: SNP array plink to VCF validation issue
21 months ago by
chrchang523
10k
1
vote
2
replies
2.3k
views
Answer:
Answer: Plink : Variant names are limited to 16000 characters
21 months ago by
chrchang523
10k
1
vote
1
reply
2.2k
views
Answer:
Answer: High proportion of non-biallelic SNPs in dbSNP 155 vs 144
21 months ago by
chrchang523
10k
1
vote
1
reply
2.9k
views
Answer:
Answer: set-all-var-ids misuse in plink 2.0
21 months ago by
chrchang523
10k
2
votes
2
replies
1.1k
views
Answer:
Answer: Changing from "rs" to "chr_pos_ref_alt"
21 months ago by
chrchang523
10k
2
votes
1
reply
650
views
Answer:
Answer: PRS with multiple panels of SNP weights
21 months ago by
chrchang523
10k
1
vote
1
reply
1.3k
views
Answer:
Answer: updating .bim with new rsids
22 months ago by
chrchang523
10k
1
vote
1
reply
673
views
Answer:
Answer: plink update .bim question
22 months ago by
chrchang523
10k
1
vote
1
reply
805
views
Answer:
Answer: How can I keep INFO value when convert bgen to VCF by using plink2?
22 months ago by
chrchang523
10k
2
votes
1
reply
931
views
Answer:
Answer: Plink runtime when using "--extract"
23 months ago by
chrchang523
10k
442 results • Page
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