Moderator: chrchang523

gravatar for chrchang523
chrchang5233.5k
Reputation:
3,480
Status:
Trusted
Location:
United States
Last seen:
2 hours ago
Joined:
4 years, 6 months ago
Email:
c**********@gmail.com

Posts by chrchang523

<prev • 314 results • page 1 of 32 • next >
0
votes
1
answer
95
views
1
answers
Comment: C: When should you left-align INDELs (and why?)
... Either will work (as long as you aren't using a very old bcftools version). The latest bcftools should be faster, especially if compiled with "libdeflate". ...
written 5 days ago by chrchang5233.5k
5
votes
1
answer
95
views
1
answers
Answer: A: When should you left-align INDELs (and why?)
... Suppose one of your VCF files has a non-left-aligned insertion, represented as REF=AG, ALT=AGT, starting at position 99999, and another file has an insertion represented as REF=G, ALT=GT, starting at position 100000. If you don't left-align, these may not be recognized as the same variant, and down ...
written 6 days ago by chrchang5233.5k
0
votes
2
answers
4.3k
views
2
answers
Comment: C: Multisample VCF file to Structure file format ?
... The problem is the surrounding double-quotes. They're ignored by Excel, but practically every VCF file reader will complain. ...
written 14 days ago by chrchang5233.5k
0
votes
2
answers
4.3k
views
2
answers
Comment: C: Multisample VCF file to Structure file format ?
... plink does not allow "." blank POS values. Replace that column with zeroes. ...
written 14 days ago by chrchang5233.5k
0
votes
1
answer
140
views
1
answers
Comment: C: What does NA imply in a plink.raw file for genotype calling?
... Yes, it is necessary to use plink 2.0 and --make-pgen/--pfile if you want to keep track of decimal values and export them with "--recode AD". ...
written 25 days ago by chrchang5233.5k
2
votes
1
answer
113
views
1
answers
Answer: A: Triallelic variant - GWAS
... Do you know how the genotypes were initially measured? If the third allele could be expected to be systematically mistaken for one of the first two, you should adjust your interpretation of the result accordingly. But if the third allele legitimately doesn’t seem to be in your dataset and is gener ...
written 25 days ago by chrchang5233.5k
1
vote
1
answer
115
views
1
answers
Comment: C: Can we skip --mind?
... That version number doesn’t entirely make sense. While “—mind 1” would solve your immediate problem, I’d look for a way to get plink reinstalled. ...
written 27 days ago by chrchang5233.5k
0
votes
1
answer
115
views
1
answers
Answer: A: Can we skip --mind?
... What version of plink are you using? Automatic —mind was turned off ~10 years ago... ...
written 27 days ago by chrchang5233.5k
0
votes
1
answer
159
views
1
answers
Answer: A: Beagle imputation - duplication position error
... plink’s —list-duplicate-vars flag was created specifically to address this Beagle 4 issue. ...
written 4 weeks ago by chrchang5233.5k
0
votes
0
answers
274
views
0
answers
Comment: C: Converting VCF to PLINK .bed binary fileset to check for pedigree errors with KI
... No, the .bed file does not contain any pedigree/sample information; it's nothing but a matrix of {0, 1, 2, missing} allele count values. (Even the matrix dimensions aren't in the file!) ...
written 4 weeks ago by chrchang5233.5k

Latest awards to chrchang523

Appreciated 5 days ago, created a post with more than 5 votes. For A: Weir And Cockerham Fst from PLINK(bed/bim/fam) input files
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
Scholar 6 days ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
Teacher 6 days ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
Scholar 24 days ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: PLINK 1.90 alpha
Appreciated 5 weeks ago, created a post with more than 5 votes. For A: Weir And Cockerham Fst from PLINK(bed/bim/fam) input files
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
Scholar 8 weeks ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
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?
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?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
Scholar 5 months ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
Scholar 5 months ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
Scholar 6 months ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
Good Answer 7 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?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
Scholar 8 months ago, created an answer that has been accepted. For A: Alternetive to GoldenHelix GWAS
Scholar 8 months ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1509 users visited in the last hour