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Search: Posts Made By: shyam_la
Forum: Bioinformatics 05-13-2014, 06:36 AM
Replies: 2
Views: 1,978
Posted By shyam_la
For everyone's info, I contacted the developers. ...

For everyone's info, I contacted the developers.

The issue was because I was using Windows and they had a bug that confused forward vs backward slashes in path names. They fixed it and released a...
Forum: Bioinformatics 05-08-2014, 12:07 PM
Replies: 2
Views: 1,978
Posted By shyam_la
Exclamation Virmid - SNV mutation caller

Anyone here have any experience using Virmid? I have some exome seq data that I want to use it on but on first attempt with default parameters I get this error:

Exception in thread "main"...
Forum: Bioinformatics 12-03-2012, 05:10 AM
Replies: 5
Views: 2,929
Posted By shyam_la
Justin, That is exactly what I wanted to...

Justin,

That is exactly what I wanted to know; mutate each codon and get the result. Thank you!
But I'm guessing 1:3.17 is not a biologically meaningful ratio because typically cancers (which is...
Forum: Bioinformatics 11-28-2012, 06:52 AM
Replies: 5
Views: 2,929
Posted By shyam_la
Query on NonSilent and Silent mutations..

What is the ratio of non-silent to silent mutations resulting from single nucleotide substitutions that can be expected, if every base is equally mutable and there is no selection pressure?

Hope...
Forum: Bioinformatics 09-12-2012, 01:21 PM
Replies: 5
Views: 1,659
Posted By shyam_la
No I meant a BAM file in place of a fasta file..

No I meant a BAM file in place of a fasta file..
Forum: Bioinformatics 09-12-2012, 11:53 AM
Replies: 5
Views: 1,659
Posted By shyam_la
Thank you. Will try that out.. Is it possible to...

Thank you. Will try that out.. Is it possible to do a similar thing with an aligned sorted BAM file?
Forum: Bioinformatics 09-12-2012, 08:21 AM
Replies: 5
Views: 1,659
Posted By shyam_la
Question Question of retrieving nucleotides from a list of genomic coordinates..

Lets say I have an excel file, one column with chr number and the next with genomic coordinates, running into several thousands in numbers. Is there some online / offline tool into which I can input...
Forum: Bioinformatics 09-06-2012, 05:57 AM
Replies: 2
Views: 1,501
Posted By shyam_la
Thank you. They seem to be fairly complicated to...

Thank you. They seem to be fairly complicated to use.. Will give them a shot..
Forum: Bioinformatics 08-24-2012, 09:48 AM
Replies: 2
Views: 1,501
Posted By shyam_la
Need help with CNV..

Hi,

I'm relatively new to bioinformatics. Have mastered SNVs and indels for the most part.. Now want to try my hand with CNVs.. I'm working with tumor-normal exome data..

My question is, is it...
Forum: Bioinformatics 08-24-2012, 05:44 AM
Replies: 5
Views: 1,894
Posted By shyam_la
I have a related question: Can the copy number...

I have a related question: Can the copy number algorithm of VarScan still be used if my tumor and normal data are sequenced to varying depths? Lets says mean tumor depth is 2.5 times mean normal...
Forum: Bioinformatics 08-22-2012, 11:14 AM
Replies: 34
Views: 10,159
Posted By shyam_la
Having the exact same problem. Anybody come up...

Having the exact same problem. Anybody come up with a solution yet? I use Win 7 64 bit as my native OS. Hence the VM.. Also I am getting the same error when I use cygwin..
Forum: Bioinformatics 08-14-2012, 04:15 PM
Replies: 7
Views: 2,223
Posted By shyam_la
No, not currently, as far as I know.. May I ask...

No, not currently, as far as I know.. May I ask why you specifically want it in vcf format?
Forum: Bioinformatics 08-05-2012, 11:42 PM
Replies: 7
Views: 2,223
Posted By shyam_la
It appears you have used MuTect to call your...

It appears you have used MuTect to call your SNVs. The current beta version of MuTect is very verbose and the initial output is more than a hundred fold bigger than it should be.

use "grep -v...
Forum: Bioinformatics 08-03-2012, 12:13 AM
Replies: 1
Views: 1,751
Posted By shyam_la
It says "Out of memory". Try increasing Xmx2g to...

It says "Out of memory". Try increasing Xmx2g to Xmx3g or Xmx4g, to assign more java heap space and try again..
Forum: Bioinformatics 07-31-2012, 10:07 AM
Replies: 7
Views: 1,796
Posted By shyam_la
Yeah, exactly my thoughts.. Thank you.

Yeah, exactly my thoughts..
Thank you.
Forum: Bioinformatics 07-30-2012, 01:45 PM
Replies: 7
Views: 1,796
Posted By shyam_la
Did it on 1 sample.. Got 2492 SNVs (exons only)...

Did it on 1 sample..
Got 2492 SNVs (exons only) vs 2768 (exons + 10 bp).
78% of those were annotated as exonic/splicing vs 70% (exon + 10bp)..

So, 8% of the difference is due to the extra 10bp...
Forum: Bioinformatics 07-30-2012, 09:08 AM
Replies: 7
Views: 1,796
Posted By shyam_la
HI, 1) On IGV, they are not very different...

HI,

1) On IGV, they are not very different at the genomic level.. If I zoom in to look at finer details, the NimbleGen one has a lot of exons missing that are present in the refseq one (which is...
Forum: Bioinformatics 07-30-2012, 09:04 AM
Replies: 7
Views: 1,796
Posted By shyam_la
Yes, the 2100 are included in the 2700. Of course...

Yes, the 2100 are included in the 2700. Of course the bed files vary - but that is not an explanation for my observation..
Forum: Bioinformatics 07-27-2012, 03:01 PM
Replies: 7
Views: 1,796
Posted By shyam_la
Exclamation Exome Analysis.. Annotation - unusual observation; need explanation..

I have a bioinformatics query on the exome project we are running. We are using a NimbleGenV2 exome capture kit for target capture.

It's a unusual sort of question, and has been nagging me for...
Forum: Bioinformatics 07-26-2012, 03:04 PM
Replies: 16
Views: 2,565
Posted By shyam_la
But is that relevant in this context?? ...

But is that relevant in this context??
Assuming you have now understood my question..
Forum: Bioinformatics 07-26-2012, 01:16 PM
Replies: 16
Views: 2,565
Posted By shyam_la
Can you please explain?

Can you please explain?
Forum: Bioinformatics 07-25-2012, 06:37 PM
Replies: 16
Views: 2,565
Posted By shyam_la
Script doesn't work really. Still stuck with no...

Script doesn't work really. Still stuck with no solution in sight..
Forum: Bioinformatics 07-25-2012, 05:37 PM
Replies: 16
Views: 2,565
Posted By shyam_la
They are actually in standard UCSC refgene txt...

They are actually in standard UCSC refgene txt fomat. If you go to table browser, and try to export all fields in selected table as plain text, thats the kind of file. But the file that annovar uses...
Forum: Bioinformatics 07-25-2012, 05:17 PM
Replies: 16
Views: 2,565
Posted By shyam_la
I tested a few more loci. Annovar and IGV compare...

I tested a few more loci. Annovar and IGV compare well, on intron vs exon, but not so well when its UTR5/UTR3 vs exon.. Some UTR annotated sites fall within IGV exons..

I don't think...
Forum: Bioinformatics 07-25-2012, 04:59 PM
Replies: 16
Views: 2,565
Posted By shyam_la
Well, I just picked 10 random spots from the list...

Well, I just picked 10 random spots from the list and tested them individually.. Half the time the annotation is correct (comparing to IGV), half the time its not..

I can't draw any conclusions...
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