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Forum: Bioinformatics 08-25-2016, 05:15 AM
Replies: 3
Views: 1,887
Posted By geertvandeweyer
good question. It's not my VCF, so I was...

good question. It's not my VCF, so I was wondering the same thing...
Forum: Bioinformatics 08-25-2016, 01:04 AM
Replies: 3
Views: 1,887
Posted By geertvandeweyer
VCF specification question

Hi,

I couldn't find this in the VCF specification documents. Is it allowed to have two lines in a VCF with the same variant, identical format & sample columns but different info fields?

edit:...
Forum: Bioinformatics 08-18-2016, 10:26 PM
Replies: 0
Views: 1,206
Posted By geertvandeweyer
allele order in phased VCF

Hi all,

I know related issues have been discussed before, but I can't find an answer to this specific question:

if you have a phased VCF file, how do the AD fields relate?

would you for...
Forum: Bioinformatics 04-18-2016, 02:12 AM
Replies: 0
Views: 2,188
Posted By geertvandeweyer
PySAM VCF : add new filter

Hi,

I'm trying to add a new filter to a VCF file after processing using pysam. I can add new format fields to the output header using :

vcf_file = pysam.VariantFile(vcf_path)
new_header =...
Forum: Sample Prep / Library Generation 04-20-2015, 04:26 AM
Replies: 1
Views: 1,827
Posted By geertvandeweyer
Dual Indexing for NimbleGen SeqCap

Hi all,

For all here performing dual indexed panel resequencing: We just published an adaptation of the seqCap protocol to allow dual indexing and 96 sample multiplexing.

For details, see:
...
Forum: Metagenomics 08-04-2013, 01:15 AM
Replies: 1
Views: 1,866
Posted By geertvandeweyer
Advies on tool selection

Hi,

I was asked to provide tools in a local galaxy instance to handle the following research question:

Two groups of microbial cultures taken from case and control animals, were 16S sequences...
Forum: General 05-16-2013, 07:42 AM
Replies: 0
Views: 1,109
Posted By geertvandeweyer
Available Control Trio Exomes

Hi,

I'm looking for publicly available data from some (healthy) trios to use as internal validation runs. AFAIK, the ESP data is not publicly availalbe, and the sample list of 1KG does not list...
Forum: Bioinformatics 05-15-2013, 08:44 AM
Replies: 1
Views: 1,192
Posted By geertvandeweyer
Afaik this Walker is remplaceer by The BQSR...

Afaik this Walker is remplaceer by The BQSR Walker.

See: http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_bqsr_BaseRecalibrator.html

Best

Geert
Forum: Bioinformatics 08-13-2012, 06:44 AM
Replies: 8
Views: 90,673
Posted By geertvandeweyer
Hi, I've attached my approach to...

Hi,

I've attached my approach to demultiplexing the MiSeq files. Note that it uses the MiSeq assigned sample idx to name the output files, NOT the barcode. This means you get all reads for the...
Forum: Illumina/Solexa 08-06-2012, 12:27 AM
Replies: 1
Views: 2,013
Posted By geertvandeweyer
HiSeq 2000 BCL-converter sys. req.

Hi,

We are awaiting the installation of a HiSeq system on our site, and are investigating ICT requirements. We are especially looking for hands-on experience on the following items, as the...
Forum: Bioinformatics 06-19-2012, 02:21 AM
Replies: 13
Views: 16,598
Posted By geertvandeweyer
To dig up an old thread: I believe the perl...

To dig up an old thread: I believe the perl approach to this function does not fit with the (correct) graphical interpretation that was provided here. As can be seen on the attached plots, reads will...
Forum: Bioinformatics 02-03-2011, 07:26 AM
Replies: 4
Views: 2,431
Posted By geertvandeweyer
I finally managed to take a look at your...

I finally managed to take a look at your questions. Please retry you query on the website. You will notice that the output has changed for csv results. For each supplied rs_ID, the dbSNP frequencies...
Forum: Bioinformatics 01-26-2011, 12:30 AM
Replies: 4
Views: 2,431
Posted By geertvandeweyer
The page was updated to query based on rs-ID and...

The page was updated to query based on rs-ID and do batch processing.
Forum: Bioinformatics 01-17-2011, 05:02 AM
Replies: 4
Views: 2,431
Posted By geertvandeweyer
1KG online data querying

Hi all,

For those interested, we have put online a 1KG data querying website.

Variation can be retrieved based on position, gene name or sequence.
Results are population frequency, total...
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