User: chrchang523

gravatar for chrchang523
chrchang5232.9k
Reputation:
2,900
Status:
Trusted
Location:
United States
Last seen:
7 hours ago
Joined:
4 years, 2 months ago
Email:
c**********@gmail.com

Posts by chrchang523

<prev • 276 results • page 1 of 28 • next >
2
votes
2
answers
88
views
2
answers
Answer: A: Where to download official reference and alternative alleles from 1000 Genomes?
... See ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ for 1000 Genomes phase 3 VCFs, and ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ for phase 1. Phase 1 plink-formatted files with reference alleles in the 6th .bim column can be downloaded from https://www.cog-genomics.org/p ...
written 7 days ago by chrchang5232.9k
0
votes
1
answer
108
views
1
answers
Comment: C: Plink: compute LD between all SNP pairs
... If you remove inter-chr, you need to manually specify large values for ld-window and ld-window-kb. ...
written 21 days ago by chrchang5232.9k
0
votes
1
answer
108
views
1
answers
Answer: A: Plink: compute LD between all SNP pairs
... "--r2 inter-chr --ld-window-r2 0" reports all results in table format, while "--r2 square" generates a text matrix. ...
written 22 days ago by chrchang5232.9k
0
votes
1
answer
91
views
1
answers
Answer: A: update fam file VCF -> plink bfile
... --update-parents (http://www.cog-genomics.org/plink/1.9/data#update_indiv ), --update-sex, and --pheno can be used for this purpose. ...
written 22 days ago by chrchang5232.9k
0
votes
1
answer
133
views
1
answers
Answer: A: PLINK IBD calculation for given samples against the rest of the data
... This isn't directly supported by plink 1.9. However, if M is large enough that it isn't reasonable to just perform the entire computation and then filter for the lines of interest, the following hack will help: 1. Create a file (I'll call this id_order.txt) which has the M sample IDs of interest o ...
written 24 days ago by chrchang5232.9k
1
vote
1
answer
92
views
1
answers
Answer: A: vcftools/ plink conserve phase information
... plink 2.0 can do this, but you may still lose some other types of information in the VCF. Have you tried bcftools? ...
written 29 days ago by chrchang5232.9k
0
votes
0
answers
169
views
0
answers
Comment: C: PLINK input files not found (adds .fam to input.bed)
... You need to get your hands on the .bim and .fam that originally accompanied the .bed, then. ...
written 5 weeks ago by chrchang5232.9k
0
votes
0
answers
169
views
0
answers
Comment: C: PLINK input files not found (adds .fam to input.bed)
... What genotype files do you have? Neither .bed nor .ped files make sense on their own; plink .bed files must be accompanied by a .bim and a .fam file, while plink .ped files must be accompanied by a .map. ...
written 5 weeks ago by chrchang5232.9k
0
votes
1
answer
215
views
1
answers
Comment: C: Convert vcf files with phased genotypes to standard haplotype format
... plink2 codes the REF allele as 1 and the ALT allele as 0 in the .haps file. If they don't always correspond to the ancestral/derived allele distinction you want, you can use --ref-allele or --alt1-allele (https://www.cog-genomics.org/plink/2.0/data#ref_allele ) to swap them around when necessary (y ...
written 5 weeks ago by chrchang5232.9k
3
votes
1
answer
215
views
1
answers
Answer: A: Convert vcf files with phased genotypes to standard haplotype format
... Assuming all of your genotypes are phased, this should be doable with recent plink 2.0 alpha builds (which you can download from https://www.cog-genomics.org/plink/2.0/ ): plink2 --vcf phased.vcf --export haps --out new_filename_prefix ...
written 5 weeks ago by chrchang5232.9k

Latest awards to chrchang523

Teacher 21 days ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
Scholar 5 weeks ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
Scholar 5 weeks ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
Scholar 12 weeks ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
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?
Scholar 4 months ago, created an answer that has been accepted. For A: SNP-set enrichment in GWAS analysis
Scholar 4 months ago, created an answer that has been accepted. For A: Alternetive to GoldenHelix GWAS
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
Scholar 4 months ago, created an answer that has been accepted. For A: Alternetive to GoldenHelix GWAS
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
Teacher 5 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: Alternetive to GoldenHelix GWAS
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
Scholar 6 months ago, created an answer that has been accepted. For A: Alternetive to GoldenHelix GWAS
Scholar 6 months ago, created an answer that has been accepted. For A: Alternetive to GoldenHelix GWAS
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: PLINK 1.90 alpha
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
Appreciated 7 months ago, created a post with more than 5 votes. For A: Alternetive to GoldenHelix GWAS
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: List of np-hard problems in biology/bioinformatics
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
Appreciated 8 months ago, created a post with more than 5 votes. For A: Alternetive to GoldenHelix GWAS
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: 1368 users visited in the last hour