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Search: Posts Made By: binfoUser
Forum: Bioinformatics 03-27-2018, 05:57 AM
Replies: 0
Views: 554
Posted By binfoUser
Combined effect of variants

I would like to know if there is some tool or database where I can analyze the effect of co-occurring variants in the DNA.
Forum: Bioinformatics 10-28-2016, 08:34 AM
Replies: 8
Views: 1,975
Posted By binfoUser
I don't know the pipeline used to identify the...

I don't know the pipeline used to identify the variants. The only thing that I have access to is the reference file used, that was: hg38.fa
The variants are saved in a VCF file. What I want to do is...
Forum: Bioinformatics 10-28-2016, 08:17 AM
Replies: 8
Views: 1,975
Posted By binfoUser
But I only have the file with the variants...

But I only have the file with the variants already identified, nothing else. And due to the nomenclature, some variants can't be annotated by their genomic coordinates.
Forum: Bioinformatics 10-28-2016, 08:05 AM
Replies: 8
Views: 1,975
Posted By binfoUser
Do you mean the reference used to find the...

Do you mean the reference used to find the variants in the sequence? Or the reference used by the annotation software?
Forum: Bioinformatics 10-28-2016, 06:59 AM
Replies: 8
Views: 1,975
Posted By binfoUser
Software to annotate variants

I am wondering if there is any software that annotates variants not by the variants genomic coordinates but by their position in the cDNA.

Thank you
Forum: Bioinformatics 09-07-2016, 01:01 AM
Replies: 2
Views: 1,699
Posted By binfoUser
I need data from patients, it doesn't matter the...

I need data from patients, it doesn't matter the disease or condition. I'm looking for data that was analysed by someone before and it's available online, kind of a repository. I don't know if that...
Forum: Bioinformatics 09-06-2016, 02:55 AM
Replies: 2
Views: 1,699
Posted By binfoUser
Exome data available

Does anyone know if there is exome data available from patients? I mean data to be used for variants analysis.
Forum: Bioinformatics 03-21-2016, 07:17 AM
Replies: 1
Views: 1,035
Posted By binfoUser
How to access SNPedia in Java

I'm accessing diferent databases to collect data for different variants found in a human sequence. One of the databases that I want to use is SNPedia. But I can't find any API to use. Is there a...
Forum: Bioinformatics 03-18-2016, 02:14 AM
Replies: 1
Views: 904
Posted By binfoUser
This kind of information (population diversity)...

This kind of information (population diversity) is too big to access via eUtils. It needs to be downloded and parsed
Forum: Bioinformatics 03-14-2016, 09:05 AM
Replies: 1
Views: 904
Posted By binfoUser
Access population diversity in dbSNP

I want to access dbSNP database with java and obtain the population diversity. The first thing that I did was to use eUtils (Entrez Programming Utilities) by NCBI. With this I can access specific...
Forum: Bioinformatics 02-23-2016, 08:58 AM
Replies: 6
Views: 896
Posted By binfoUser
Each line represents a variant found in the DNA...

Each line represents a variant found in the DNA sequence, so if I specify a region present in the file the algorithm has to return that region.
It's strange not to work for the whole file.
Forum: Bioinformatics 02-23-2016, 04:21 AM
Replies: 6
Views: 896
Posted By binfoUser
Yes it does. The first result is 47588 and the...

Yes it does. The first result is 47588 and the last 48249.
Forum: Bioinformatics 02-23-2016, 04:13 AM
Replies: 6
Views: 896
Posted By binfoUser
It's for human. Chromosome is from 47588 to...

It's for human. Chromosome is from 47588 to 133787425. If I search in the beginning of the chromosome, it gives no problem. But if I search in the middle it does not return anything.
Forum: Bioinformatics 02-23-2016, 02:15 AM
Replies: 6
Views: 896
Posted By binfoUser
Library Htsjdk to query a vcf file

I'm using VCFFileReader file= new VCFFileReader(file.vcf, file.vcf.gz.tbi, true) to open a file and then CloseableIterator<VariantContext> vc = file.query("10", 77162995, 131048262) to query...
Forum: Bioinformatics 02-16-2016, 02:21 AM
Replies: 1
Views: 1,417
Posted By binfoUser
This is the code that I have so far: ...

This is the code that I have so far:

VCFFileReader fileR= new VCFFileReader(f, fi, true);
VCFHeader fileHeader = fileR.getFileHeader();
VCFRecordCodec recCodec = new VCFRecordCodec(fileHeader);...
Forum: Bioinformatics 02-16-2016, 01:23 AM
Replies: 1
Views: 1,417
Posted By binfoUser
How to use .tbi for vcf file

I want to use indexed vcf files. For that I have a file .vcf and another file .tbi
I don't know how to use .tbi file. I'm using htsjdk library for Java but I don't know which methods to use.
For...
Forum: Bioinformatics 01-08-2016, 12:45 AM
Replies: 2
Views: 2,168
Posted By binfoUser
But the VCFHeader only access the file header and...

But the VCFHeader only access the file header and it gives me that line that you showed with id "CSQ". But now I want to extract the info added that is present in the data lines after the header.
I...
Forum: Bioinformatics 01-06-2016, 01:32 AM
Replies: 2
Views: 2,168
Posted By binfoUser
Using library htsjdk vcf files

I want to analyse VCF files that have annotations. I used programs like VEP to annotate the file and now I want to see and manipulate these annotations that are in the file.
I'm using a Java library...
Forum: Bioinformatics 01-05-2016, 12:32 PM
Replies: 6
Views: 3,742
Posted By binfoUser
It worked! But I was reading this page building...

It worked! But I was reading this page building htsjdk (http://samtools.github.io/htsjdk/building.html#BuildingHtsJdk) and it was talking about 1.6. I was confused because of that.

Thank you!
Forum: Bioinformatics 01-05-2016, 08:50 AM
Replies: 6
Views: 3,742
Posted By binfoUser
I think is this: [javac]...

I think is this:

[javac] /home/usr/Documents/htsjdk-master/build.xml:241: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
...
Forum: Bioinformatics 01-05-2016, 08:40 AM
Replies: 6
Views: 3,742
Posted By binfoUser
I saw that library but I have to use Ant to build...

I saw that library but I have to use Ant to build the jarfile. I installed Ant and when I run the code to buil the jar I get an error:

BUILD FAILED...
Forum: Bioinformatics 01-05-2016, 07:43 AM
Replies: 6
Views: 3,742
Posted By binfoUser
Java library to manipulate VCF files

I'm starting to work with VCF files and other types of files with genes annotation.
I want to know if there is any Java libraries that I can use to manipulate vcf files.

Thank you!
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