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Search: Posts Made By: spreeth84
Forum: Bioinformatics 02-11-2015, 06:59 AM
Replies: 3
Views: 3,835
Posted By spreeth84
Hi swe, I have had better luck with Mutect than...

Hi swe, I have had better luck with Mutect than Haplotype caller or Unified Genotyper for calling low frequency alterations. There are parameters that can be further tweaked in Mutect to achieve...
Forum: Bioinformatics 05-17-2012, 02:26 PM
Replies: 3
Views: 3,835
Posted By spreeth84
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
Posted By spreeth84
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
Posted By spreeth84
it turned out I had to set Downsampling to None....

it turned out I had to set Downsampling to None. My AD and DP were under reported due to the downsampling.
Forum: Bioinformatics 03-27-2012, 03:43 PM
Replies: 3
Views: 5,362
Posted By spreeth84
The Reordering can be done only after sorting -...

The Reordering can be done only after sorting - you will still have to first sort your reads (and reference) by coordinates. Guess that doesn't solve the reference sorting problem you are facing..
Forum: Bioinformatics 03-27-2012, 02:43 PM
Replies: 3
Views: 5,362
Posted By spreeth84
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
Posted By spreeth84
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
Posted By spreeth84
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
Posted By spreeth84
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...
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