Re: [galaxy-user] Genomic interval file for GATK

2011-12-12 Thread Praveen Raj Somarajan
? Has anybody experienced/resolved this before? Thanks, Raj. From: Carlos Borroto [mailto:carlos.borr...@gmail.com] Sent: Thursday, December 08, 2011 7:43 PM To: Praveen Raj Somarajan Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Genomic interval file for GATK Hi Raj, I've

Re: [galaxy-user] Genomic interval file for GATK

2011-12-08 Thread Carlos Borroto
Hi Raj, I've been also testing GATK Beta pipeline on Galaxy. This is the workflow I have so far: http://test.g2.bx.psu.edu/u/cjav/w/gatk There are a few error coming up that I haven't had the time to fix or work around yet, but I think it could be a good starting point. For example an issue with

[galaxy-user] Genomic interval file for GATK

2011-12-07 Thread Praveen Raj Somarajan
All, I'm using a locally installed galaxy with GATK 1.3 beta (recently updated). I would be interested in variant calling using GATK on both Illumina and SOLiD data. My questions are: 1) What should be the format that "Genomic Interval" option can accept in beta version. It produced an error