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 when I provided an (enrichment coords) bed file? DepthOfCoverage had also produced error when I used bed files. Would beta release (v1.3) accept bed file as input for genomic intervals?

2) SAMtool index is seem to be missing in Galaxy. Is this true or any other module (say SAM->BAM) incorporates this functionality?

Looking forward to your comments.

Raj

This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment.

The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system.

OCIMUMBIO SOLUTIONS (P) LTD