Forum: Bioinformatics
03-08-2018, 12:52 AM
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Replies: 0
Views: 641
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:...
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Forum: Bioinformatics
07-07-2015, 09:42 AM
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Replies: 0
Views: 1,016
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Forum: Bioinformatics
11-06-2014, 01:01 AM
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Replies: 0
Views: 1,076
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 ...
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Forum: Bioinformatics
08-21-2014, 03:07 AM
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Replies: 0
Views: 1,842
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...
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Forum: Bioinformatics
11-02-2013, 01:19 PM
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Replies: 0
Views: 825
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...
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Forum: Bioinformatics
04-12-2013, 12:30 AM
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Replies: 11
Views: 3,418
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...
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Forum: Bioinformatics
01-26-2013, 11:21 AM
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Replies: 2
Views: 2,465
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...
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Forum: Bioinformatics
01-26-2013, 09:40 AM
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Replies: 2
Views: 2,465
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Forum: Bioinformatics
01-02-2013, 04:46 AM
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Replies: 15
Views: 7,245
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Forum: Bioinformatics
09-20-2012, 05:57 AM
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Replies: 1
Views: 1,246
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Forum: Bioinformatics
09-19-2012, 11:41 PM
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Replies: 1
Views: 1,246
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,...
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Forum: Bioinformatics
09-19-2012, 11:26 PM
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Replies: 1
Views: 1,752
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...
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Forum: Bioinformatics
08-28-2012, 03:04 AM
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Replies: 0
Views: 1,162
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...
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Forum: Bioinformatics
07-16-2012, 12:37 PM
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Replies: 4
Views: 5,360
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Forum: Bioinformatics
07-16-2012, 03:44 AM
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Replies: 7
Views: 7,837
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Forum: Bioinformatics
07-13-2012, 08:36 AM
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Replies: 2
Views: 1,629
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...
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Forum: Bioinformatics
07-12-2012, 11:26 PM
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Replies: 15
Views: 7,245
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Forum: Bioinformatics
06-14-2012, 02:01 PM
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Replies: 8
Views: 2,454
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...
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Forum: Bioinformatics
06-14-2012, 10:13 AM
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Replies: 9
Views: 2,900
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...
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Forum: Bioinformatics
06-14-2012, 10:07 AM
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Replies: 5
Views: 2,712
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...
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Forum: Bioinformatics
02-04-2012, 05:07 AM
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Replies: 4
Views: 2,545
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...
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Forum: Bioinformatics
12-21-2011, 12:16 AM
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Replies: 4
Views: 2,545
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Forum: Bioinformatics
01-23-2011, 08:10 AM
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Replies: 2
Views: 3,184
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...
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Forum: Bioinformatics
01-23-2011, 07:54 AM
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Replies: 2
Views: 2,475
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...
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Forum: Bioinformatics
01-18-2011, 08:12 AM
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Replies: 2
Views: 2,475
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....
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