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Forum: Bioinformatics 02-01-2013, 06:11 AM
Replies: 22
Views: 12,152
Posted By oliviajm
Is it fixed in all VarScan tools? Which one...

Is it fixed in all VarScan tools?

Which one do you use?

I use VarScan.v2.3.4.jar mpileup2indel and I still get some "C +AAAG" or "G -AT" in my vcf output file.


Olivia
Forum: Bioinformatics 02-01-2013, 04:00 AM
Replies: 22
Views: 12,152
Posted By oliviajm
Hello all, I realised that the missing qual...

Hello all,

I realised that the missing qual field had been added in one of the last versions of VarScan. As I use it in a pipeline, I did not update it recently to avoid compatibility problems.
...
Forum: Bioinformatics 01-29-2013, 11:08 PM
Replies: 22
Views: 12,152
Posted By oliviajm
Hi Thon, I've solved the problem by writing...

Hi Thon,

I've solved the problem by writing a small script to convert the files obtained with VarScan in the "right" vcf format. By this way, it's OK with Annovar.

Concerning the str10 values...
Forum: Bioinformatics 09-13-2012, 08:04 AM
Replies: 22
Views: 12,152
Posted By oliviajm
Hi, I'm wondering if it's valid vcf too. ...

Hi,

I'm wondering if it's valid vcf too.
Actually, the vcf format in the varscan output looks like
...
Forum: Bioinformatics 06-08-2012, 12:07 AM
Replies: 1
Views: 1,329
Posted By oliviajm
Sample name inn VarScan vcf output file

Hi everyone,

I was wondering if there was a way to indicate to VarScan the names of the samples that would appear in the header of the vcf output file as columns names in stead of "Sample 1",...
Forum: Bioinformatics 06-07-2012, 11:46 PM
Replies: 4
Views: 4,997
Posted By oliviajm
Hi Olga, if you're still interested in using...

Hi Olga,

if you're still interested in using a vcf file, I've seen that the latest version of VarScan can output a vcf file with the otpion --output-vcf.

Olivia
Forum: Bioinformatics 06-07-2012, 11:41 PM
Replies: 5
Views: 4,415
Posted By oliviajm
Hi Mark, I got a similar problem with...

Hi Mark,

I got a similar problem with another software when I tried to provide it with a vcf file coming from VarScan mpileup2indel. It seems that in the vcf files obtained with VarScan the QUAL...
Forum: Bioinformatics 04-13-2012, 01:18 AM
Replies: 8
Views: 1,092
Posted By oliviajm
Hi, I have run some others tests, with and...

Hi,

I have run some others tests, with and without the option MINIMUM_ALLELE_PROBABILITY=1. And I'm not sure of what it does.

When the minimum allele probability value is 1 instead of the...
Forum: Bioinformatics 04-11-2012, 12:30 AM
Replies: 8
Views: 1,092
Posted By oliviajm
I'm using srma-0.1.15.jar. You can download...

I'm using srma-0.1.15.jar.

You can download a file containing the chr1 lines of the SAM file I'm using there: http://dl.free.fr/vcBPNsKpn
SRMA crashed at this level on my last try (Records...
Forum: Bioinformatics 04-10-2012, 06:33 AM
Replies: 8
Views: 1,092
Posted By oliviajm
Hello again, I noticed that I get an error...

Hello again,

I noticed that I get an error every time that I have run several SRMA on the same input file at the same time but with different options and different output files.
Is it possible...
Forum: Bioinformatics 04-02-2012, 11:22 PM
Replies: 8
Views: 1,092
Posted By oliviajm
Thank you for answering so soon. I've seen the...

Thank you for answering so soon.
I've seen the warning, but my problem is not about the time now. I would like to understantd why it doesn't work any more when I had an option.

I made another...
Forum: Bioinformatics 04-02-2012, 03:34 AM
Replies: 8
Views: 1,092
Posted By oliviajm
SRMA problem with NUM_THREADS

Hello,

I've run SRMA without any error on a file, but it last 74 hours. So I would like to use the NUM_THREADS option. But when I tried, I get this mesage :

[Fri Mar 30 16:08:54 CEST 2012]...
Forum: Introductions 04-02-2012, 03:15 AM
Replies: 373
Views: 109,871
Posted By oliviajm
Hi from France

Hello everybody,

I'm from Lille, North of France. I work on NGS since 1 month only, but I hope for a long time.

Thanks for this very useful forum.
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