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.
Regards.
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.
Regards.
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