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Old 07-12-2013, 07:39 PM   #1
Location: moon

Join Date: Nov 2012
Posts: 19
Default Pindel multi sample run

Hi All,

I am running Pindel with multiple samples together and it's certainly giving some amazing results. Thanks to Kai Ye for such a nice tool. Now I have a mixed bag of bam files produced from sequences generated in different batches. My question is: can I use multiple bam files from different batches together in Pindel? Will the CNV predictions be affected by different coverages of bam files from different batches? If yes, what should I do in this case? Should I just run the bam files from the same batch together? Or does it not really matter? I hope my questions are making some sense.

Many thanks in advance.

opulcy97 is offline   Reply With Quote
Old 07-15-2013, 06:40 AM   #2
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Location: amsterdam

Join Date: Jun 2009
Posts: 133

Pindel combines read-pair and split-read, which are also affected by the amount of data at any given region. You can certainly mix bam files from different batches and Pindel will find the variants as long as there is any supporting evidence in one sample and appear in other samples in the cohort.

when you run pindel on a large amount of samples, please use -w to control memory usage.
KaiYe is offline   Reply With Quote
Old 07-18-2013, 12:52 AM   #3
Location: moon

Join Date: Nov 2012
Posts: 19

Hi Kai Ye,

Thanks for the reply. It makes more sense now.

opulcy97 is offline   Reply With Quote

muti sample run, pindel

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