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Search: Posts Made By: vivek_
Forum: Bioinformatics 05-10-2019, 12:18 AM
Replies: 4
Views: 337
Posted By vivek_
I'd suggest raising an issue on the GATK support...

I'd suggest raising an issue on the GATK support forums. One of the other issues I had been encountering with GATK4 is that there is a discordance between the command line options in the online...
Forum: Bioinformatics 10-25-2018, 12:44 AM
Replies: 1
Views: 588
Posted By vivek_
The easiest way would be to align the sequence...

The easiest way would be to align the sequence using BLAT: https://genome.ucsc.edu/cgi-bin/hgBlat?command=start

If its a handful of bases you can use mutalyzer's position converter:...
Forum: Bioinformatics 09-03-2018, 12:27 AM
Replies: 2
Views: 829
Posted By vivek_
You could set it to 0 and not have any issues as...

You could set it to 0 and not have any issues as long as 1 & 4 are accurate.
Forum: Bioinformatics 08-26-2018, 11:57 PM
Replies: 5
Views: 852
Posted By vivek_
Beta is the effect size.

Beta is the effect size.
Forum: Bioinformatics 08-24-2018, 01:23 AM
Replies: 5
Views: 852
Posted By vivek_
Does it not have a Beta? If you have a z-score...

Does it not have a Beta? If you have a z-score and p-value you can compute a beta from them using inverse probability transformation. You can read up on this online and get a formula to do so.
Forum: Bioinformatics 08-24-2018, 12:13 AM
Replies: 5
Views: 852
Posted By vivek_
You'll have to search the highest powered GWAS of...

You'll have to search the highest powered GWAS of T2D and download the association results. That's the base file on which you are going to build the predictive model.
Forum: Bioinformatics 07-21-2017, 02:50 AM
Replies: 5
Views: 1,210
Posted By vivek_
If it complains about quality scores, you can...

If it complains about quality scores, you can just generate a file with some dummy scores. I'm not sure how it would handle one read per sample though. You can also try samtools for variant calling...
Forum: Bioinformatics 07-21-2017, 12:45 AM
Replies: 5
Views: 1,210
Posted By vivek_
You could likely use BWA-Mem to do the alignment...

You could likely use BWA-Mem to do the alignment and call variants using the GATK's UnifiedGenotyper module.
Forum: Bioinformatics 06-14-2017, 12:30 AM
Replies: 1
Views: 497
Posted By vivek_
This is super neat. Great work.

This is super neat. Great work.
Forum: Introductions 03-06-2017, 11:59 PM
Replies: 2
Views: 865
Posted By vivek_
Welcome aboard. :)

Welcome aboard. :)
Forum: Bioinformatics 02-23-2017, 05:58 AM
Replies: 3
Views: 781
Posted By vivek_
You can try this

You can try this
Forum: Bioinformatics 02-23-2017, 05:53 AM
Replies: 3
Views: 781
Posted By vivek_
Gives you the headers If your entire...

Gives you the headers

If your entire sequence is in one line, you can use



to select all sequences belonging to that organism.
Forum: Bioinformatics 01-27-2017, 02:15 AM
Replies: 4
Views: 1,140
Posted By vivek_
If hard filtering is what you want to do, you can...

If hard filtering is what you want to do, you can simply write scripts to parse the VCF and either modify the QUAL column in the VCF or simply exclude variants.

However the GATK's variant...
Forum: Bioinformatics 01-25-2017, 02:55 AM
Replies: 6
Views: 1,547
Posted By vivek_
GATK is one of the best documented software in...

GATK is one of the best documented software in Bioinformatics, are you even making an effort to go to their webpage and reading tutorials or documentation?
Forum: Bioinformatics 01-24-2017, 12:29 AM
Replies: 6
Views: 1,547
Posted By vivek_
The GATK distribution is a jar file, it should...

The GATK distribution is a jar file, it should run if you have java installed.
Forum: Bioinformatics 12-12-2016, 02:16 AM
Replies: 11
Views: 7,059
Posted By vivek_
I used to have a MacBook Air but recently bought...

I used to have a MacBook Air but recently bought an MBP and my workload is pretty similar.

I ssh into the institute cluster for any memory intensive tasks so the only things I run locally on my...
Forum: Bioinformatics 12-01-2016, 06:32 AM
Replies: 1
Views: 1,172
Posted By vivek_
Adding 1000 genomes samples might be...

Adding 1000 genomes samples might be counterintuitive because you probably already use them as a training set to build the VQSR classifier. There shouldn't be an issue with using hard filtering but...
Forum: Bioinformatics 12-01-2016, 06:26 AM
Replies: 1
Views: 1,072
Posted By vivek_
You can get the descriptions from a readme file...

You can get the descriptions from a readme file included in the dbNSFP distribution.

https://sites.google.com/site/jpopgen/dbNSFP
Forum: General 09-02-2016, 03:31 AM
Replies: 2
Views: 960
Posted By vivek_
I don't think there is a filter involved in the...

I don't think there is a filter involved in the conversion, anyways you should get a .log file that tells you all that annovar did on the dataset.
Forum: Bioinformatics 08-25-2016, 05:20 AM
Replies: 3
Views: 1,316
Posted By vivek_
Looks like it is a different alternate allele. So...

Looks like it is a different alternate allele. So the VCF is inaccurate.

http://exac.broadinstitute.org/dbsnp/rs1058172
Forum: Bioinformatics 08-25-2016, 05:05 AM
Replies: 3
Views: 1,316
Posted By vivek_
How do you get different allele allele...

How do you get different allele allele frequencies in ExAC for the same alternate allele and location?
Forum: Bioinformatics 08-16-2016, 12:10 AM
Replies: 1
Views: 1,101
Posted By vivek_
Depending on the size of structural variants...

Depending on the size of structural variants genotyping does not have a straightforward solution. Pindel can give you genotypes for smaller events (upto 100bp) but with larger events (> 1kb), even...
Forum: General 06-03-2016, 11:52 AM
Replies: 5
Views: 1,214
Posted By vivek_
Oh well, re-reading his post, it appears like he...

Oh well, re-reading his post, it appears like he wants to keep the same username but have a different display name appear next to his posts.
Forum: General 06-03-2016, 07:26 AM
Replies: 5
Views: 1,214
Posted By vivek_
Who do you want to delete it? I had an account...

Who do you want to delete it? I had an account with a crappy username when I was a student, I just abandoned it and signed up to a new account with my first name afterwards.
Forum: Bioinformatics 05-06-2016, 06:38 AM
Replies: 10
Views: 1,775
Posted By vivek_
I have reposted the code.

I have reposted the code.
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