gatk python script

[m_elena_bioinfo]

Hi NGS users,
anyone could say me where i can find the python script of GATK (ConvertTableToAnnotatorRod.py, GenerateTranscriptToInfo.py...)?

Thanks a lot,
ME

[raonyguimaraes]

Yes I know where you can get, the problem is that it's not public yet

https://svn.broadinstitute.org/Sting/branches/expIndelInUG/python/genomicAnnotatorScripts/GenerateTranscriptToInfo.py

[m_elena_bioinfo]

thanks a lot.
I have to generate rod file for depth coverage in all exon of all genes in a whole-exome bam file (according to http://www.broadinstitute.org/gsa/wi...It_Was_Created instruction).
Any idea about fix this problem?

[raonyguimaraes]

So I guess we are trying to do the same analysis

I think, you don't need rod files anymore, you should use VCF files instead

To calculate the depth of coverage:

http://www.broadinstitute.org/gsa/wiki/index.php/Depth_of_Coverage_v3.0

You will need:

-R /path/to/your/reference.fasta
-I /path/to/your/bam_file.bam
-o /path/to/your/output_file

And the intervals ...

-L /path/to/your/intervals.interval_list

[m_elena_bioinfo]

You are right, we are performing the same analysis.
Ok, I'm already using the depth coverage v3.
As interval list what do you use?
I have a whole exome. Can I use the bed file?
How can i select the specific gene for calculate the coverage in each single exon?

Thanks a lot again!!!!
:-)

[svl]

I'm still looking at an efficient way to do this too. I use samtools view and perl to create a table for each sample (.bam) with for each region (so in this case exon coordinates):

- average coverage in region
- percentage bases covered by at least 1
- percentage bases covered by at least 5
- etc

But still searching for a way to store this efficiently while being able to compare it between any sample (whether whole-exome or any other capture design). If you do it for each exon, there's around 600.000 of them to calculate the stats for..

[Seq84]

You are right, we are performing the same analysis.
Ok, I'm already using the depth coverage v3.
As interval list what do you use?
I have a whole exome. Can I use the bed file?
How can i select the specific gene for calculate the coverage in each single exon?

Thanks a lot again!!!!
:-)

Yes sure you can use the .bed file. You should have a .bed file with all targeted regions (exons regions). Set in depthofcoverage the option -L exons.bed.
If you want to have a specific coverage (of exons) for each gene you can provide an interval list with custom coordinates of the exons of your gene.

Instead if you want only the coverage of all genes use the option -genelist.

[frymor]

If you want to have a specific coverage (of exons) for each gene you can provide an interval list with custom coordinates of the exons of your gene.

Hi,

is it also possible to use the GRanges object from the R package GenomicRanges as an interval list of exons/gernes?

Thanks

A.