User: Molly_K

gravatar for Molly_K
Molly_K20
Reputation:
20
Status:
New User
Location:
United States
Last seen:
5 months, 1 week ago
Joined:
4 years ago
Email:
k******@gmail.com

Posts by Molly_K

<prev • 5 results • page 1 of 1 • next >
0
votes
1
answer
337
views
1
answers
Comment: C: vcftools: unwanted filtering
... I basically realized it's a misunderstanding on my end so I deleted the question, realizing it isn't even a good question, but if someone has the same doubt when interpreting the results, this post may be helpful :P ...
written 6 months ago by Molly_K20
1
vote
1
answer
337
views
1
answers
Answer: C: vcftools: unwanted filtering
... I just realized that the larger number represents the SNPs that are not on the specified chromosome, they are not relevant lol.. thanks so much for thinking with me. I checked the output files (chr22) and compare with the original if I just use awk to get chr22, the row numbers are the same, ha. I w ...
written 6 months ago by Molly_K20
0
votes
1
answer
337
views
1
answers
Comment: C: vcftools: unwanted filtering
... @genomax, thank you for the suggestion. I did read the vcftool manual but there isn't anything describing what are the default filtering values. I thought I was just breaking down the large file to smaller files, it shouldn't be doing any filtering. I read through the options carefully but didn't se ...
written 6 months ago by Molly_K20
3
votes
1
answer
337
views
1
answer
vcftools: unwanted filtering
... I am using vcftools to breakdown a large VCF file into smaller files using - for i in `seq 1 22`; do vcftools --gzvcf ~/path_to_large.vcf.gz --chr "$i" --out ~/path_to_small_vcf --recode; done This is the message I got after running this command (using chr22 as example) VCFtools - 0.1.15 ...
vcftools snp written 6 months ago by Molly_K20
1
vote
1
answer
1.5k
views
1
answer
Permutation using Plink
... I'd like to generate the permutation data from genotype among 200 samples using PLINK. To create this file, I ran permutation of case/control labels in a GWAS experiment and recalculate the p-values of all SNPs under all permutations. I did 50 times permutations. ./plink --file 1000G_EUR --assoc ...
permutation plink snp written 2.8 years ago by Molly_K20 • updated 5 months ago by Shicheng Guo6.5k

Latest awards to Molly_K

Scholar 6 months ago, created an answer that has been accepted. For C: vcftools: unwanted filtering
Popular Question 20 months ago, created a question with more than 1,000 views. For Permutation using Plink

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1804 users visited in the last hour