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.


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