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Forum: Bioinformatics 09-09-2013, 08:07 AM
Replies: 1
Views: 2,799
Posted By ElenaN
VarScan somatic indel caller working incorrectly?

Hi
I am seeing a seemingly incorrect somatic indel call using VarScan somatic.
The VarScan output line is
chr2 178883096 T +TAAC 11 0 0% T 6 2 25% */+TAAC Somatic 1 0.16374269 6 0 2 0 9 2 0 0
...
Forum: Bioinformatics 07-03-2013, 01:43 AM
Replies: 4
Views: 5,845
Posted By ElenaN
Thanks, Dan! :) (BTW, I just posted another...

Thanks, Dan! :)
(BTW, I just posted another VarScan question as a separate thread http://seqanswers.com/forums/showthread.php?p=109364#post109364 - it'd be really great if you could answer it as...
Forum: Bioinformatics 07-03-2013, 01:39 AM
Replies: 1
Views: 3,387
Posted By ElenaN
VarScan: somatic mutations in heterozygous sites?

Does VarScan2 find somatic mutations that arose in loci where norm was heterozygous? As far as I can tell, it classifies somatic changes as "Somatic" (but that seems to only include homozygous...
Forum: Bioinformatics 06-13-2013, 03:17 AM
Replies: 2
Views: 21,782
Posted By ElenaN
bwa mem segfault; bwa bwasw breaks MarkDuplicates

Hi,
I have run into various problems with various versions of bwa
1. bwa mem gives a segmentation fault right away. Not sure how to debug that, no matter what memory (we have 48G) and thread...
Forum: Bioinformatics 06-13-2013, 03:05 AM
Replies: 5
Views: 8,817
Posted By ElenaN
Thanks. So the -b value should be what the user...

Thanks.
So the -b value should be what the user considers to be a reasonable cutoff?
Forum: Bioinformatics 06-06-2013, 03:21 AM
Replies: 5
Views: 8,817
Posted By ElenaN
bam-readcount usage

Hi, could someone tell me what is the proper way to run bam-readcount (for later use with the VarScan2 fpfilter.pl?)
Specifically, what should be the "list of regions to report readcounts within"...
Forum: Bioinformatics 06-06-2013, 12:54 AM
Replies: 4
Views: 5,845
Posted By ElenaN
Filtering steps for VarScan2 somatic and germline calls

What is the proper filtering pipeline for somatic mutation detection using VarScan2, with tumor/normal paired samples?
My understanding of the steps:
0. VarScan2 somatic to make calls
Then filter:...
Forum: Genomic Resequencing 11-30-2012, 06:00 AM
Replies: 0
Views: 1,395
Posted By ElenaN
Illumina vs NimbleGen for exome sequencing

Hi,
We are deciding between Illumina's TruSeq and NimbleGen's SeqCap EZ v 3.0 exome kits, and would appreciate any insight to help us make the decision.
We plan to perform exome sequeincing in two...
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