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Forum: Bioinformatics 03-08-2018, 12:52 AM
Replies: 0
Views: 641
Posted By krawitz
image flow cytometry

Dear all,
is IFC the next big thing? Does anyone know about a map that lists the sites with image flow cytometers, e.g. from Amnis?
A few years ago, I found this threat and paper very helpful:...
Forum: Bioinformatics 07-07-2015, 09:42 AM
Replies: 0
Views: 1,016
Posted By krawitz
multiple vcf file from BaseSpace

Hi,
does anyone know how to generate a multiple vcf file in BaseSpace?
Thanks a lot!
Peter
Forum: Bioinformatics 11-06-2014, 01:01 AM
Replies: 0
Views: 1,076
Posted By krawitz
ExAC

Hi folks,
the exome aggregation consortium, ExAC (http://exac.broadinstitute.org/), just made genotype data of more than 65,000 exomes available. We updated GeneTalk's ...
Forum: Bioinformatics 08-21-2014, 03:07 AM
Replies: 0
Views: 1,842
Posted By krawitz
phasing de novo mutations

Hi folks,

Let's suppose I called the variants in a parent child trio and filtered for de novo mutations in the child. I am now interested in the phase, that is, I would like to know whether the...
Forum: Bioinformatics 11-02-2013, 01:19 PM
Replies: 0
Views: 825
Posted By krawitz
find the second patient

To solve the molecular genetics of an unknown genetic disorder usually two or more unrelated patients with the same phenotype and mutations in the same gene are required. However, as most of these...
Forum: Bioinformatics 04-12-2013, 12:30 AM
Replies: 11
Views: 3,418
Posted By krawitz
You could also try the following: upload your...

You could also try the following:
upload your multiple vcf file to GeneTalk (www.gene-talk.de). Use the collection tool to asign all the cases the status "affected" and all the controls the status...
Forum: Bioinformatics 01-26-2013, 11:21 AM
Replies: 2
Views: 2,465
Posted By krawitz
example

the example of NA12878 with the two POS is:

10 46999406 . A G . . . 1/1
10 46999406 . AGGG AGGGAGGTGGGGG 0/1

In my opinion one of the called genotypes must be an artifact, as...
Forum: Bioinformatics 01-26-2013, 09:40 AM
Replies: 2
Views: 2,465
Posted By krawitz
VCF multiple records with the same POS, why?

Hi,
I stumbled upon two entries in the VCF of NA12878 with the same position. I thought this is not allowed. I checked the vcf specifications at...
Forum: Bioinformatics 01-02-2013, 04:46 AM
Replies: 15
Views: 7,245
Posted By krawitz
I agree annovar and SNPeff seem to be most widely...

I agree annovar and SNPeff seem to be most widely used for variant annotation. For variant analysis there are e.g. ingenuity (commercial), annotate-it and www.gene-talk.de. We are using GeneTalk at...
Forum: Bioinformatics 09-20-2012, 05:57 AM
Replies: 1
Views: 1,246
Posted By krawitz
already solved by vcf-merge from vcftools

I did my homework:
that is exactly the kind of output vcf-merge from vcftools produces,...
Forum: Bioinformatics 09-19-2012, 11:41 PM
Replies: 1
Views: 1,246
Posted By krawitz
How to combine indels in VCF - a puzzle

Hi,
here is a puzzle for VCF cracks! How do you combine 2 vcf files, where one of them has an insertion and the other one a deletion at the same position. Let's say the reference sequence is caag,...
Forum: Bioinformatics 09-19-2012, 11:26 PM
Replies: 1
Views: 1,752
Posted By krawitz
There is now the "left align" convention in...

There is now the "left align" convention in reporting indels. In vcf you describe an insertion by reporting the last unchanged base you from the left that is for sure. Let's assume your reference...
Forum: Bioinformatics 08-28-2012, 03:04 AM
Replies: 0
Views: 1,162
Posted By krawitz
Platform independent quality assessment of Exomes

Hi,
we are working on a platform independent score to assess the quality of an exome. We predict the genotyping accuracy of the exome simply based on the composition of the variant set. Is anyone...
Forum: Bioinformatics 07-16-2012, 12:37 PM
Replies: 4
Views: 5,360
Posted By krawitz
www.gene-talk.de can do the annotation for you....

www.gene-talk.de can do the annotation for you. all you have to do is uploading your vcf. it is a free annotation, filtering and interpretation tool for human sequence variants.
Forum: Bioinformatics 07-16-2012, 03:44 AM
Replies: 7
Views: 7,837
Posted By krawitz
You might also want to try www.gene-talk.de . It...

You might also want to try www.gene-talk.de . It is an wiki-like expert platform for filtering and annotating sequence variants. The automatic annotation is based on annovar. For the interpreation of...
Forum: Bioinformatics 07-13-2012, 08:36 AM
Replies: 2
Views: 1,629
Posted By krawitz
How to include coverage information in vcf

Hi folks

When we report variants in vcf format a common question is: what is
the coverage profile of the target region? Combining vcf and coverage
information allows to deduce also the genotypes...
Forum: Bioinformatics 07-12-2012, 11:26 PM
Replies: 15
Views: 7,245
Posted By krawitz
You might want to try www.gene-talk.de

You might want to try www.gene-talk.de
Forum: Bioinformatics 06-14-2012, 02:01 PM
Replies: 8
Views: 2,454
Posted By krawitz
If you have your data in vcf format you could...

If you have your data in vcf format you could also give GeneTalk a try. It basically uses annovar for functional annotations. Besides you can also filter for pathogenic variants annotated by the...
Forum: Bioinformatics 06-14-2012, 10:13 AM
Replies: 9
Views: 2,900
Posted By krawitz
Hi Shyam_la, GeneTalk is designed for non...

Hi Shyam_la,
GeneTalk is designed for non Bioinformaticians analyzing human sequence variants. So this might be an option for you. Who gave you the data? There is a standard format for reporting...
Forum: Bioinformatics 06-14-2012, 10:07 AM
Replies: 5
Views: 2,712
Posted By krawitz
Hi Caswater, in GeneTalk's (www.gene-talk.de)...

Hi Caswater,
in GeneTalk's (www.gene-talk.de) vcfViewer you will see the number of individuals with the same genotype from the 1000 genomes and 5000 exomes project.
Is this what you were looking...
Forum: Bioinformatics 02-04-2012, 05:07 AM
Replies: 4
Views: 2,545
Posted By krawitz
the samtools mpileup output can be piped into...

the samtools mpileup output can be piped into VarScan to apply a coverage and frequency filter:
samtools pileup -f reference.fasta myData.bam | java -jar VarScan.v2.2.jar pileup2snp --min-coverage...
Forum: Bioinformatics 12-21-2011, 12:16 AM
Replies: 4
Views: 2,545
Posted By krawitz
A heretically simple approach to variant calling

Hi everyone,

we had a look at the distribution of heterozygous allele frequencies in NGS datasets and found that their variance is larger than expected by a bionomial distribution...
Forum: Bioinformatics 01-23-2011, 08:10 AM
Replies: 2
Views: 3,184
Posted By krawitz
how to call snps with samtools from 454.bam

Hi there,

I really like samtools for variant calling on Illumina.bam. However, now I have a GS Junior 454 data set. I aligned the reads via bwa bwasw and got a .sam alignment. I converted to .bam...
Forum: Bioinformatics 01-23-2011, 07:54 AM
Replies: 2
Views: 2,475
Posted By krawitz
The following options in samtools will call...

The following options in samtools will call genotypes even, if they agree with the reference:
samtools mpileup -f <ref.fa> -l <PositionsToGenotype> -cg <alignment.bam> >genotypes.bcf
bcftools view...
Forum: Bioinformatics 01-18-2011, 08:12 AM
Replies: 2
Views: 2,475
Posted By krawitz
How to Call Genotypes on NGS datasets for linkage

Hi there,
there are several decent variant callers for NGS data sets, such as samtools, GATK, ... that report variants to a reference in vcf4.0 format. These are well suited for variant detection....
Showing results 1 to 25 of 30

 


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