SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 9 of 9
Search took 0.00 seconds.
Search: Posts Made By: MolecularToast
Forum: Bioinformatics 10-22-2012, 09:53 AM
Replies: 15
Views: 7,687
Posted By MolecularToast
If anyone is still listening to this thread -...

If anyone is still listening to this thread - what versions of bwa is everyone using who is getting this error?
Forum: Bioinformatics 07-17-2012, 06:49 AM
Replies: 0
Views: 902
Posted By MolecularToast
BAM2MPG Exome Target File

Hello,

Does anyone know how to feed bam2mpg an actual bed file of target regions? There is a --region option but I can't get it to work with an actual file. It seems to be set up to work like...
Forum: Bioinformatics 12-20-2011, 07:04 AM
Replies: 0
Views: 1,570
Posted By MolecularToast
NextGENe and VCF

Does anyone know if NextGENe software will output a variant list in VCF format? And if not, does anyone have a script to convert a NextGENe variant list into VCF?

Thanks
Forum: Bioinformatics 03-02-2011, 12:14 PM
Replies: 1
Views: 2,074
Posted By MolecularToast
Bfast index splitting and appropriate hash width

I am creating colorspace reference indexes with bfast and need to split them using the "-d" argument (only 16GB of RAM). Something like this:

$BFAST/bfast index -f $REF -m 1111111111111111111111...
Forum: Bioinformatics 12-08-2010, 06:53 PM
Replies: 2
Views: 4,824
Posted By MolecularToast
Converting Dindel VCF file to GATK BED file

Does anyone have a script or know of one that is capable of converting the VCF file output of Dindel into the BED format output of the GATK's IndelGenotyper?

From this:
...
Forum: Bioinformatics 11-17-2010, 07:39 AM
Replies: 6
Views: 5,580
Posted By MolecularToast
Thank you - I did end up running it on a linux...

Thank you - I did end up running it on a linux box with about 4x the comp power and 4x the RAM and it did speed it up (comparatively) quite a bit (at least within my tolerable range).

Thank you...
Forum: Bioinformatics 11-08-2010, 12:28 PM
Replies: 6
Views: 5,580
Posted By MolecularToast
Thank you both for your replies. I tried...

Thank you both for your replies. I tried increasing the MAX_RECORDS_IN_RAM once and all it seemed to do was create larger temp files that merged just as slowly. I'll try passing even more RAM to...
Forum: Bioinformatics 11-07-2010, 09:42 AM
Replies: 6
Views: 5,580
Posted By MolecularToast
FixMateInformation after GATK realignment

I'm using GATK to analyze some paired-end Illumina exome data and have been running into a problem after realignment using IndelRealigner. After realignment, I have been trying to use Picard's...
Forum: Introductions 10-02-2010, 01:28 PM
Replies: 0
Views: 1,010
Posted By MolecularToast
Greetings and Salutations

Pretty psyched when I found this resource! Big thanks to the creators, moderators, and contributors.

Haven't fully explored previous posts but would be greatly appreciative if anyone could send...
Showing results 1 to 9 of 9

 


All times are GMT -8. The time now is 07:41 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO