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Forum: Bioinformatics 07-13-2015, 05:03 AM
Replies: 1
Views: 2,401
Posted By chrisamiller
Several solutions are presented in this thread: ...

Several solutions are presented in this thread:
https://www.biostars.org/p/6553/

These include a GATK walker:...
Forum: Genomic Resequencing 01-31-2014, 05:13 AM
Replies: 1
Views: 1,530
Posted By chrisamiller
VarscanHighConfidence is in the FT field. That's...

VarscanHighConfidence is in the FT field. That's the name of the filter that removed that site (it failed the filter that retains high-confidence SNPs).
Forum: Bioinformatics 11-27-2013, 06:39 AM
Replies: 1
Views: 1,540
Posted By chrisamiller
FWIW, there are reasonably good instructions for...

FWIW, there are reasonably good instructions for installing MuSiC here:

http://gmt.genome.wustl.edu/genome-shipit/genome-music/current/
http://www.biostars.org/p/62793/

There are a ton of...
Forum: Bioinformatics 08-08-2013, 05:56 AM
Replies: 1
Views: 1,901
Posted By chrisamiller
It's a challenging issue that usually requires...

It's a challenging issue that usually requires several steps:

1) local assembly to identify the exact sequence of the large indel
2) creation of a contig containing that sequence
3) competitive...
Forum: Bioinformatics 08-05-2013, 06:04 AM
Replies: 5
Views: 9,350
Posted By chrisamiller
Succinctly, you expect heterozygous somatic SNVs...

Succinctly, you expect heterozygous somatic SNVs to be present in a sample at a frequency around 50% (and homozygous changes to be present at 100%). If your tumor is impure, these fractions will...
Forum: Genomic Resequencing 05-06-2013, 10:46 AM
Replies: 3
Views: 7,891
Posted By chrisamiller
This thread explains the -r vs -l issue. The -l...

This thread explains the -r vs -l issue. The -l is not using the bam index:
...
Forum: General 08-12-2009, 12:10 PM
Replies: 67
Views: 80,403
Posted By chrisamiller
Baylor College of Medicine is mislabeled on your...

Baylor College of Medicine is mislabeled on your map. It's in Houston, TX, not Waco (we're unaffiliated with Baylor University). Here's a map of the correct location:
...
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