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I am running an analysis on TCGA bam files (GCRh37/hg19) of whole exome sequencing data.

I usually find one bam file for each sample. However, at least one sample has two bam files, in which the last part of the name (before the extension) has the suffix .1 or .2 or .3...

For example, C500.TCGA-BL-A3JM-01A-12D-A21A-08.1.bam and C500.TCGA-BL-A3JM-01A-12D-A21A-08.2.bam.

I didn't find an explanation for this last suffix. Are they duplicates, or.. ? Is there some wiki about the last part of the filename?

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If you check the bam list of TCGA, you'll see that they use different numbers for the bam files (maybe different settings). What the difference is, I don't know, but if you want the file that they used for their paper, it is C500.TCGA-BL-A3JM-01A-12D-A21A-08.2.bam, the other one is not in the list.

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