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Old 10-09-2013, 06:41 AM   #19
Location: Hong Kong

Join Date: Feb 2012
Posts: 21

From my memory, you should be able to get a bam file from the TableRecalibration. From what I understand, you only have to merge samples (as in, really merge samples into one single bam file) when you sequence the same sample on multiple lane. You can refer to the following:

And also the best practice link that I have previously attached. According to my labmates, they said merging the bam file made it difficult to analyse downstream as it will be a huge file (e.g. 4 6GB bam merged will become ~24GB). All in all, I'd really recommend you reading the best practice guide from GATK, they cover most stuff you need to know.

As for the bed file, it is just for removing SNPs in areas that shouldn't be captured by the kit. So most of the time, you should focus only on the capture areas. However, if you don't have that information and couldn't get it from the people, then you can consider using only the exome part from the UCSC. I have never tried that but I guess you can, my recommendation is to always get the capture information from the people and make sure you know what you are working with.
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