User: Kantale

gravatar for Kantale
Kantale120
Reputation:
120
Status:
Trusted
Location:
Groningen, Netherlands
Website:
http://www.pypedia.com
Last seen:
3 weeks, 6 days ago
Joined:
8 years, 8 months ago
Email:
a********************@gmail.com

Posts by Kantale

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Difference in Hardy-Weinberg Equilibrium (HWE) between subpopulations and the to
... Thank you for your reply. BTW I posted this also in [reddit][1] and I received more or else the same comments. I believe that these difference are indeed due to population structure. [1]: https://www.reddit.com/r/bioinformatics/comments/jk95t1/difference_in_hardyweinberg_equilibrium_hwe/ ...
written 29 days ago by Kantale120
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Difference in Hardy-Weinberg Equilibrium (HWE) between subpopulations and the total population
... I am examining the HWE on 6 HLA genes (A, B, C, DRB1, DQB1, DPB1) in a population which has 2 subpopulations (municipalities). I am using Arlequin v 3.5.2.2 for the HWE test using unphased genotypes. The p-values in one of the HLA genes (B) on the total population is 0.002, on subpopulation 1 is 0. ...
hwe hla population genetics written 4 weeks ago by Kantale120
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Comment: C: How Can I Compute The R Square Hat Statistic For Imputed Data?
... Hi, I came here by accident after a long time and saw your post. Sorry for the delay. The scripts are available here: https://github.com/kantale/scripts/blob/e6e48ee3a514a7a4fa2b40479925e0ee635e897c/imputation/imputation_quality_metrics.py ...
written 8 months ago by Kantale120
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Comment: C: A questionnaire regarding reproducibility and collaboration issues on bioinforma
... Thank you for your feedback. Note taken! ...
written 21 months ago by Kantale120
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Forum: A questionnaire regarding reproducibility and collaboration issues on bioinformatics
... Hi, In [my department](https://www.ics.forth.gr/cbml/) we have just started a new project called [OpenBio-C](https://www.openbio.eu/) which aims to develop a new collaborative Tool repository and Workflow Management System for the bioinformatics community. In order to steer the development towards ...
collaboration questionnaire forum reproducibility written 21 months ago by Kantale120
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Answer: A: Converting Between Impute2 And Ped/Map After Imputation - 1St Column Dashes Prob
... Also take a look at this python implementation: http://www.pypedia.com/index.php/Convert_impute2_gprobs_to_PEDMAP_beagle_user_Kantale From the long parameter list, you can only define the following parameters: chromosome, input_impute2_gprobs_filename, input_impute2_info_filename, output_TPED ...
written 6.6 years ago by Kantale120 • updated 11 months ago by _r_am31k
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Answer: A: Imputation Using 1000 Genome Phase I V3
... It would be very helpful to mention which software are you using. About your first question: If you use IMPUTE2 then you can use the complete 1000 Genome reference panel. IMPUTE2 will try to find the best subset of the reference population based on your study panel. Imputation with IMPUTE2 even wi ...
written 6.6 years ago by Kantale120 • updated 11 months ago by _r_am31k
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Answer: A: Understanding Imputed Genotypes
... Hi, It seems that the numbers that you have are dosages. Dosage is a simple linear transformation of the posterior genotype probabilities usually coming from imputation. Assuming that you have a SNP: A/B and your genotype probabilities are: A/A: 0.1 A/B: 0.4 B/B: 0.5 (They should all ...
written 6.6 years ago by Kantale120 • updated 11 months ago by _r_am31k
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Comment: C: Genotype Imputation And Population Substructure
... I agree with Genotepes. You can do imputation with IMPUTE2, then use the complete HapMap reference panel and don't care about the population structure at all! IMPUTE2 includes algorithms to choose the optimum subset of the reference panel for you. This is better than making a subset of the populat ...
written 6.6 years ago by Kantale120 • updated 11 months ago by _r_am31k
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Answer: A: Association Tests Using Impute2 Output
... I know that you said that you want to perform association analysis with plink, but I would recommend to try SNPTEST. The reason is that since you did the imputation with IMPUTE2, SNPTEST can process (relatively) nicely IMPUTE2 output files. You can use QCTOOL to convert IMPUTE2 output to SNPTEST inp ...
written 6.6 years ago by Kantale120 • updated 11 months ago by _r_am31k

Latest awards to Kantale

Appreciated 21 months ago, created a post with more than 5 votes. For A: Understanding Imputed Genotypes
Good Answer 21 months ago, created an answer that was upvoted at least 5 times. For A: Understanding Imputed Genotypes
Popular Question 6.5 years ago, created a question with more than 1,000 views. For How Can I Compute The R Square Hat Statistic For Imputed Data?
Teacher 6.5 years ago, created an answer with at least 3 up-votes. For A: Understanding Imputed Genotypes
Supporter 6.6 years ago, voted at least 25 times.

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