Moderator: chrchang523

gravatar for chrchang523
chrchang5235.8k
Reputation:
5,780
Status:
Trusted
Location:
United States
Last seen:
2 hours ago
Joined:
5 years, 11 months ago
Email:
c**********@gmail.com

Posts by chrchang523

<prev • 483 results • page 1 of 49 • next >
1
vote
1
answer
58
views
1
answers
Comment: C: Problems understanding .cov files in Plink
... Yes, but when rereading that description yesterday, I realized that it was probably too terse for first-time users. So I provided a different explanation that would generate a concrete example for him to look at. I will be adding a bunch of examples to the documentation over the next several weeks ...
written 9 hours ago by chrchang5235.8k
2
votes
1
answer
58
views
1
answers
Answer: C: Problems understanding .cov files in Plink
... Answered at https://groups.google.com/forum/#!topic/plink2-users/HieqQ4DLZZQ . ...
written 21 hours ago by chrchang5235.8k
2
votes
1
answer
47
views
1
answers
Comment: C: PLINK file format case control status
... Note that ped+map has not been plink’s preferred format since 2007, and is not even supported at all by plink 2.0 alpha builds (while VCF is supported). You probably want to convert to a plink binary format (bed+bim+fam) instead. ...
written 2 days ago by chrchang5235.8k
1
vote
1
answer
2.8k
views
1
answers
Comment: C: Permutation using Plink
... That is an invalid MAP file. ...
written 4 days ago by chrchang5235.8k
0
votes
1
answer
96
views
1
answers
Answer: A: Plink allele with frequency greater than 0.05
... Use plink 2.0 —vcf to directly import the VCF when you need to keep track of REF/ALT alleles. ...
written 6 days ago by chrchang5235.8k
0
votes
1
answer
71
views
1
answers
Comment: C: Any fast way to download 1000 Genome Phase 3?
... The downloads from https://www.cog-genomics.org/plink/2.0/resources#1kg_phase3 are ~70% smaller, and contain all the information in the VCFs (“plink2 —pfile ... —export vcf bgz” can be used to generate actual VCFs). ...
written 8 days ago by chrchang5235.8k
0
votes
1
answer
57
views
1
answers
Answer: A: How to Select A Given Subset of SNPs from the 1000GP Dataset?
... The entire 1000GP phase 3 dataset is only a ~3.6 GiB download from https://www.cog-genomics.org/plink/2.0/resources , or ~3 GiB if you don't need the VCF annotations. From there, it should not be too difficult to intersect with your dataset. ...
written 9 days ago by chrchang5235.8k
2
votes
1
answer
57
views
1
answers
Answer: A: How to convert PLINK data files to bgen and bgen.bgi files?
... With PLINK 2.0, plink2 --bfile ... --export bgen-1.2 --out ... can be used to create the bgen file (replace "1.2" with "1.1" or "1.3" if you want a different format version). bgenix (https://bitbucket.org/gavinband/bgen/wiki/bgenix ) can then be used to construct the .bgen.bgi index. ...
written 12 days ago by chrchang5235.8k
0
votes
1
answer
64
views
1
answers
Answer: A: remove singletons in LD pruning in plink
... This is independent of LD pruning, you’d want to do it beforehand. plink —bfile ... —mac 2 —make-bed —out ... removes all singleton heterozygous variants. ...
written 17 days ago by chrchang5235.8k
1
vote
1
answer
109
views
1
answers
Answer: A: PCA with Plink1.9 - eigenval and eigenvec files are all 0
... Retry with plink 2.0; at minimum, it will print a relevant error message. ...
written 20 days ago by chrchang5235.8k

Latest awards to chrchang523

Scholar 11 days ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Scholar 24 days ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Scholar 3 months ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: How to I convert 23andMe Raw Genome to GenBank or FASTA?
Appreciated 4 months ago, created a post with more than 5 votes. For A: Weir And Cockerham Fst from PLINK(bed/bim/fam) input files
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: PLINK 1.90 alpha
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: How to I convert 23andMe Raw Genome to GenBank or FASTA?
Appreciated 4 months ago, created a post with more than 5 votes. For A: Weir And Cockerham Fst from PLINK(bed/bim/fam) input files
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Scholar 5 months ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: How to I convert 23andMe Raw Genome to GenBank or FASTA?
Appreciated 5 months ago, created a post with more than 5 votes. For A: Weir And Cockerham Fst from PLINK(bed/bim/fam) input files
Scholar 5 months ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Scholar 5 months ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Appreciated 5 months ago, created a post with more than 5 votes. For A: Weir And Cockerham Fst from PLINK(bed/bim/fam) input files
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'
Scholar 6 months ago, created an answer that has been accepted. For A: PLINK: Error: Invalid chromosome code 'chr11_KI0721v1_random'

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 855 users visited in the last hour