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Forum: Bioinformatics 01-12-2012, 04:44 AM
Replies: 9
Views: 8,237
Posted By doc.ramses
Thanks for your contribution I will give that a...

Thanks for your contribution I will give that a try!
Forum: Bioinformatics 01-12-2012, 02:53 AM
Replies: 9
Views: 8,237
Posted By doc.ramses
Hm - good point ! So to the get the filtering...

Hm - good point !
So to the get the filtering done correctly like suggested here (http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3) and here...
Forum: Bioinformatics 01-12-2012, 02:04 AM
Replies: 9
Views: 8,237
Posted By doc.ramses
Just to be sure I correctly understand the...

Just to be sure I correctly understand the recommendations....

If I use the "--missingValuesInExpressionsShouldEvaluateAsFailing" option should solve the problem ??
Forum: Bioinformatics 01-04-2012, 12:23 PM
Replies: 4
Views: 2,620
Posted By doc.ramses
This is the solution I'm using, now. But with a...

This is the solution I'm using, now. But with a growing sample number, this is really annoying. I thought there must be a more elegant one doing this in one step.
Forum: Bioinformatics 01-04-2012, 11:40 AM
Replies: 4
Views: 2,620
Posted By doc.ramses
hm, but how can a target certain samples ? lets...

hm, but how can a target certain samples ? lets say I have a vcf with 10 samples. how to filter only for variants overlapping in samples 1 sample 3 and sample 7 ?
Forum: Bioinformatics 01-04-2012, 07:12 AM
Replies: 4
Views: 2,620
Posted By doc.ramses
vcf filtering

I have a multi sample vcf file. How can I filter only for overlapping snps within this one vcf file.
As far as I understand, intersectBed and vcf-isec only work for different files.

Thanks a lot...
Forum: Bioinformatics 01-04-2012, 01:22 AM
Replies: 9
Views: 8,237
Posted By doc.ramses
Okay, I've come a bit further. The error is due...

Okay, I've come a bit further. The error is due to some lines in the vcf where the annotation for MQRankSum or ReadPosRankSum is missing. When I delete those, it is running fine.
Anyone an idea why...
Forum: Bioinformatics 01-02-2012, 06:27 AM
Replies: 9
Views: 8,237
Posted By doc.ramses
GATK undefined variable problem

I used GATK UnifiedGenotyper (latest build) to call variants.
Now I have a vcf-file which I want to filter. Although the corresponding fields are correctly defined in the header:
...
Forum: Bioinformatics 11-15-2011, 01:00 AM
Replies: 2
Views: 6,043
Posted By doc.ramses
snpEff & snpSIFT variant filtering

Hi,

I want to filter a .vcf file with snpSIFT and have the problem that I can't use the filter expressions described here: http://snpeff.sourceforge.net/SnpSift.html

I figured out that instead...
Forum: Bioinformatics 10-18-2011, 07:41 AM
Replies: 2
Views: 2,780
Posted By doc.ramses
Thank you for pointing this out!

Thank you for pointing this out!
Forum: Bioinformatics 10-18-2011, 04:48 AM
Replies: 2
Views: 2,780
Posted By doc.ramses
GATK update changes UnifiedGenotyper output

Hey,

recently I upgraded to the latest version (GenomeAnalysisTK-1.2-1-g33967a4) and I noticed that when I run the UnifiedGenotyper with standard settings, I don't get the "SB" value, that I need...
Forum: Bioinformatics 10-18-2011, 04:41 AM
Replies: 2
Views: 2,806
Posted By doc.ramses
Oh, of course - thanks for bringing me on track...

Oh, of course - thanks for bringing me on track again! :=)
Forum: Bioinformatics 10-14-2011, 01:30 AM
Replies: 2
Views: 2,806
Posted By doc.ramses
GATK select variants

Hi,

assume I have 2 .vcf files from 2 individual samples which I would like to combine with GATK CombineVariants function. Then I would like to filter in a way that I end up only with variants...
Forum: Bioinformatics 10-04-2011, 03:34 AM
Replies: 3
Views: 3,379
Posted By doc.ramses
Thanks for the quick fix, that works for me....

Thanks for the quick fix, that works for me. Although really slow ;)
Forum: Bioinformatics 09-13-2011, 09:59 AM
Replies: 3
Views: 3,379
Posted By doc.ramses
using snappy java in picard tools

Hey,

I have a problem using picard-tools on large files. It tells me that I don't have snappyjava in java.library.
I'm not so familiar with java. Can anyone please point me on how to fix this....
Forum: Bioinformatics 05-18-2011, 10:57 PM
Replies: 5
Views: 11,693
Posted By doc.ramses
Using the latest samtools (0.1.16) with samtools...

Using the latest samtools (0.1.16) with samtools view -bS <in.sam> <out.bam> should write you a bam file with a header.
Forum: Bioinformatics 05-05-2011, 07:24 AM
Replies: 10
Views: 7,407
Posted By doc.ramses
They will definately do. They will also have a...

They will definately do. They will also have a more detailed look on GC-content etc.. And if you're placeing a big order - let them do the job for earning the money ;)
Forum: Bioinformatics 05-05-2011, 01:32 AM
Replies: 10
Views: 7,407
Posted By doc.ramses
If you use the "exon finder" it will exactly do...

If you use the "exon finder" it will exactly do this. My advice is to ask an Agilent representative to do the design for you as earray is indeed not very handy.
Forum: Bioinformatics 05-04-2011, 02:39 PM
Replies: 10
Views: 7,407
Posted By doc.ramses
You can use accession numbers instead of gene...

You can use accession numbers instead of gene names separated by a | if I remember correctly.
Getting exon positions out of a list of gene names is e.g. possible in ensembl - BIOMART.
Forum: Bioinformatics 05-02-2011, 04:06 AM
Replies: 10
Views: 5,057
Posted By doc.ramses
Can someone send me the paper via PM ? Thank...

Can someone send me the paper via PM ?
Thank you !
Forum: Bioinformatics 04-26-2011, 04:19 AM
Replies: 1
Views: 2,208
Posted By doc.ramses
galaxy tools and samtools error

Hi,

on a local installation of the latest "galaxy-tools" I mapped with "Bowtie for Illumina" and also performed "Filter SAM". It both worked well for the 22GB big fow and rev pe reads. When...
Forum: Bioinformatics 02-03-2011, 02:56 AM
Replies: 4
Views: 3,562
Posted By doc.ramses
I like the ANNOVAR tool: ...

I like the ANNOVAR tool:

http://www.openbioinformatics.org/annovar/
Forum: Bioinformatics 01-26-2011, 02:02 AM
Replies: 4
Views: 1,541
Posted By doc.ramses
I think it's worth a try. What about not mapping...

I think it's worth a try. What about not mapping against the whole genome but only the conserved regions ? Don't know if this is a good idea or if you have the needed data for this. It's just a lucky...
Forum: Bioinformatics 01-18-2011, 08:01 AM
Replies: 6
Views: 1,510
Posted By doc.ramses
The easiest way for non-bioinformatics is to do...

The easiest way for non-bioinformatics is to do this is in MS Access. There you can generate relationship based queries. E.g. column chromosome from table 1 has to match column chromosome from table...
Forum: Bioinformatics 01-13-2011, 02:07 AM
Replies: 3
Views: 2,528
Posted By doc.ramses
You can use custom tracks in the UCSC Genome...

You can use custom tracks in the UCSC Genome Browser. http://genome.ucsc.edu/index.html
You can also setup a local installation of this, if you prefer this.
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