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Forum: Bioinformatics 07-05-2012, 11:04 AM
Replies: 3
Views: 2,644
Posted By unagaswamy
XHMM for CNV analysis

Hi,

Has anyone tried the xhmm CNV tool on exomes?

http://atgu.mgh.harvard.edu/xhmm/tutorial.shtml

I tried it on five exome bams and I always get an empty vcf file!

Thanks,
-Uma
Forum: Bioinformatics 04-04-2011, 11:38 AM
Replies: 45
Views: 21,584
Posted By unagaswamy
Hi Michael, Thanks much for your reply! Makes...

Hi Michael,
Thanks much for your reply! Makes sense!
Uma
Forum: Bioinformatics 04-01-2011, 10:58 AM
Replies: 45
Views: 21,584
Posted By unagaswamy
Hi, We have the same problem, Breakwasy chokes...

Hi,
We have the same problem, Breakwasy chokes at :


since the string is not captured in its entirity by line in load_alignments function in the breakway.sharpenedges.pl

Is there a...
Forum: Introductions 02-16-2011, 08:19 AM
Replies: 0
Views: 962
Posted By unagaswamy
create pileup based on chromosome

Is there a way to create chromosome based pileup output using samtools?
something like...
samtools pileup -cvf file.bam chr1...
Forum: Bioinformatics 11-11-2010, 06:55 AM
Replies: 9
Views: 9,810
Posted By unagaswamy
Hi Bruins, Thanks for this very useful link. It...

Hi Bruins,
Thanks for this very useful link. It definitely answers some of my questions.
-Uma
Forum: Bioinformatics 11-05-2010, 08:54 AM
Replies: 9
Views: 9,810
Posted By unagaswamy
Hi All, I generated a raw pileup for all...

Hi All,
I generated a raw pileup for all reference positions using the samtools. An exmaple record for a non-SNP position is below:
chrY 11936864 G G 51 0 60 8...
Forum: Bioinformatics 11-04-2010, 10:12 AM
Replies: 1
Views: 1,903
Posted By unagaswamy
UPDATE: This error occured because I didn't...

UPDATE:
This error occured because I didn't specify the directory as current in the msub command:


Moab was trying to write the output in a directory where I did not have permissions.
Forum: Bioinformatics 11-04-2010, 08:39 AM
Replies: 1
Views: 1,903
Posted By unagaswamy
Samtools IO error

Hi Experts,
I am trying to use samtools to remove duplicates and bad reads from a BAM file. I get the following IO error. Does this mean I don't have enough space for output generation?

Exception...
Forum: Bioinformatics 10-28-2010, 07:11 AM
Replies: 9
Views: 9,810
Posted By unagaswamy
Hi nilshomer, Thanks for the reply. We are...

Hi nilshomer,
Thanks for the reply. We are generating SAM record only for the SNP positions which does have the base quality. I am interested in the Non-SNP positions as well and hence I'm trying to...
Forum: Bioinformatics 10-25-2010, 10:03 AM
Replies: 9
Views: 9,810
Posted By unagaswamy
Hi Experts, Can anyone tell me how to extract...

Hi Experts,
Can anyone tell me how to extract the base quality from the CQ field of the BAM file? I colleague of mine mentioned that every two ASCII character corresponds to the SOLiD color space....
Forum: Bioinformatics 10-21-2010, 11:49 AM
Replies: 9
Views: 9,810
Posted By unagaswamy
Thanks for the info. Here is what I have tried...

Thanks for the info.
Here is what I have tried so far to view the file for a given sample:
samtools view filename.bam chr:start-end

For non SNP positions, I am getting the base coverage using...
Forum: Bioinformatics 10-20-2010, 07:15 AM
Replies: 9
Views: 9,810
Posted By unagaswamy
Question Extracting base coverage and quality values from BAM files

Experts,
I am interested in extracting base coverage and quality values for non SNP reads from a BAM file?
Thanks,
-Uma
Forum: Site Announcements 08-09-2010, 11:36 AM
Replies: 33
Views: 28,150
Posted By unagaswamy
Hi All, I am new to this forum. I am working on...

Hi All,
I am new to this forum. I am working on validation of SNPs using NGS. I am not sure if this is the right place to post this. I am unable to make a new post. Can you please guide me on this?...
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