Forum: Bioinformatics
02-11-2015, 06:59 AM
|
|
Replies: 3
Views: 3,835
|
|
Forum: Bioinformatics
05-17-2012, 02:26 PM
|
|
Replies: 3
Views: 3,835
Detecting low frequency mutations - GATK
I am analyzing a targeted enrichment of a Hapmap blend. I have 4 hapmap samples mixed in the ratio: 74:20:5:1
I am looking to detect variants at low frequencies (upto 0.5%).
I am using GATK for the...
|
|
Forum: Bioinformatics
03-28-2012, 08:51 AM
|
|
Replies: 2
Views: 6,368
Thanks! looks like this also happens in the...
Thanks! looks like this also happens in the Unified Genotyper in reporting the AD and DP numbers. I was struggling to explain why the DP did not match the coverage at the position and if the quality...
|
|
Forum: Bioinformatics
03-28-2012, 08:43 AM
|
|
Replies: 1
Views: 1,872
|
|
Forum: Bioinformatics
03-27-2012, 03:43 PM
|
|
Replies: 3
Views: 5,362
|
|
Forum: Bioinformatics
03-27-2012, 02:43 PM
|
|
Replies: 3
Views: 5,362
Is this what you are looking for? Picard -...
Is this what you are looking for? Picard - Reorder sam
http://picard.sourceforge.net/command-line-overview.shtml#ReorderSam
You can reorder your reads to match the order of your reference...
|
|
Forum: Bioinformatics
03-27-2012, 01:51 PM
|
|
Replies: 1
Views: 1,872
GATK reported AD and DP
I am using Unified Genotyper for SNP calling. I find that the reported Allele depths and read depths seem much lower than expected (with and without the base quality recalibration). I did the...
|
|
Forum: Bioinformatics
02-10-2012, 10:37 AM
|
|
Replies: 3
Views: 2,868
Hi , I use CLC Bio for the alignment, coverage...
Hi , I use CLC Bio for the alignment, coverage calculations and SNP detection. In some cases I use GATK to recalibrate the quality scores before SNP analysis. I find that CLC Bio aligner works well...
|
|
Forum: Bioinformatics
02-10-2012, 08:21 AM
|
|
Replies: 3
Views: 2,868
CLC bio - GATK
I have been using CLC bio for over a year and quite happy with the analysis results so far. I also find GATK very useful. It is just painful to export files from one to the other and use both. I know...
|
