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Search: Posts Made By: etorstenson
Forum: Bioinformatics 06-04-2013, 08:29 AM
Replies: 3
Views: 1,789
Posted By etorstenson
Thanks for the tip, Laura. I actually figured...

Thanks for the tip, Laura. I actually figured this out after poking around the database location and discovering that what I'm putting for the -seqfile was a directory, and needed to be set to...
Forum: Bioinformatics 06-03-2013, 02:55 PM
Replies: 3
Views: 1,789
Posted By etorstenson
Cow Annotations with ANNOVAR?

Are there any ANNOVAR experts out there?

I've got some VCFs I generated from some bos Taurus exome sequence data, and I'd like to annotate them. Following the directions on their website, I did...
Forum: Bioinformatics 01-21-2013, 08:11 AM
Replies: 6
Views: 4,631
Posted By etorstenson
The index is used as a way for a program to very...

The index is used as a way for a program to very quickly find a reasonable starting point for the relevant information. I'm assuming it's used when you want to extract reads from a particular region....
Forum: Bioinformatics 01-21-2013, 07:47 AM
Replies: 3
Views: 2,082
Posted By etorstenson
ASAP v1.1.7 Released

An updated version to ASAP has been released including a handful of bug fixes as well adding some features that might be of interest to users including:


Serial execution can now be run on...
Forum: Bioinformatics 12-06-2012, 08:56 AM
Replies: 3
Views: 2,082
Posted By etorstenson
ASAP v1.1.4 Released

We have updated ASAP to version 1.1.4. Some features that have been added since the initial release include:


Support for processing single end reads (with bwa)
Bam Summaries with QPLOT
...
Forum: Bioinformatics 08-09-2012, 03:29 PM
Replies: 1
Views: 1,291
Posted By etorstenson
What version of GATK are you using? I think...

What version of GATK are you using? I think recent versions use the vcf files.
Forum: Bioinformatics 08-09-2012, 03:28 PM
Replies: 1
Views: 2,519
Posted By etorstenson
Have a look at the pileup documentation page....

Have a look at the pileup documentation page. Each of those characters (or character groups, in some cases) represent a base or a base quality from the reads that passed your filter.
...
Forum: Bioinformatics 08-09-2012, 11:11 AM
Replies: 0
Views: 1,575
Posted By etorstenson
GATK, Homozygous Ref and GQ

When I force GATK to call SNPs that are homozygous for the reference, it fails to provide a GQ. I realize that the GQ is dependent on an estimation of the frequency of the alternate, which doesn't...
Forum: Bioinformatics 08-09-2012, 11:01 AM
Replies: 1
Views: 1,491
Posted By etorstenson
You definitely don't want -v in your bcftools...

You definitely don't want -v in your bcftools view call, it hides those invariant sites.

samtools mpileup -uf referencegenomefile eg2.sorted.bam | bcftools view -cg - | perl...
Forum: Bioinformatics 06-18-2012, 07:55 AM
Replies: 3
Views: 2,082
Posted By etorstenson
ASAP: Advanced Sequence Automated Pipeline

Introducing ASAP: Advanced Sequencing Automated Pipeline
ASAP is an open source pipeline designed to assist users in managing various jobs associated with processing HiSeq data on a cluster or in...
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