Answers.Body: <p>If you check the <a href="https://tcga-data.nci.nih.gov/docs/publications/blca_2013/BLCA.BAMlist.txt" rel="nofollow noreferrer">bam list</a> 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 <strong>C500.TCGA-BL-A3JM-01A-12D-A21A-08.2.bam</strong>, the other one is not in the list.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-11-17T09:12:10.810Z
Answers.LastActivityDate: 2017-11-17T09:12:10.810Z
Answers.UserDisplayName: benn
Body: <p>I am running an analysis on TCGA bam files (GCRh37/hg19) of whole exome sequencing data.</p>
  
  <p>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 <code>.1</code> or <code>.2</code> or <code>.3</code>...</p>
  
  <p>For example, <code>C500.TCGA-BL-A3JM-01A-12D-A21A-08.1.bam</code> and <code>C500.TCGA-BL-A3JM-01A-12D-A21A-08.2.bam</code>.</p>
  
  <p>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?</p>
  
Tags: <sam><phylogenetics><human-genome>
Title: TCGA bam file duplicates (aligned reads) and related last part of TCGA barcode
ThreadText: # TCGA bam file duplicates (aligned reads) and related last part of TCGA barcode
  
  (Asked by: username_0 on 2017-09-27)
  
  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?
  
  **Tags:** sam, phylogenetics, human-genome
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2017-11-17. Score: 3 | Accepted answer
  
  If you check the [bam list](https://tcga-data.nci.nih.gov/docs/publications/blca_2013/BLCA.BAMlist.txt) 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.
  
  
  ---
  
  