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Old 10-09-2013, 04:20 AM   #17
choishingwan
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Location: Hong Kong

Join Date: Feb 2012
Posts: 21
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There's definitely no problem in using the latest dbsnp file with the old gatk pipeline. As for the print read problem, I think that's when the version different take place. In my case, in the latest gatk program, the recalibrate will not produce a new bam file as with 2.3, instead it produce a file to use for printread to print the recalibrated file. As for your question regarding merging the file. From my experience, it is unnecessary as you can input multiple files for unifiedgenotyper using multiple -I. Though I think it is advised to call all samples together ( not sure if that's the case if the capture kit are different / the sequencing platform for each sample is different, hope someone can answer that for me)


Side note, if you are doing exome sequencing, you should get the bed file from the company stating the capture area and you won't need to make one yourself.
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