Error while calculating read depth

[Patel, Khushbu]

Hello,

I am trying to run CODEX2 on a bunch of WES bamflies (without controls). I get the following error when I try to run the code 

 

Error in value[[3L]](cond) :

  failed to open BamFile: SAM/BAM header missing or empty

  file: '/users/KP/WESData/CL-TGT-10798-human_Aligned.sorted.bam.bai'

Calls: getcoverage ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>

In addition: Warning messages:

1: In .Seqinfo.mergexy(x, y) :

  The 2 combined objects have no sequence levels in common. (Use

  suppressWarnings() to suppress this warning.)

2: In doTryCatch(return(expr), name, parentenv, handler) :

  [bam_header_read] EOF marker is absent. The input is probably truncated.

3: In doTryCatch(return(expr), name, parentenv, handler) :

  [bam_header_read] invalid BAM binary header (this is not a BAM file).

Execution halted

My bam files are sorted, and indexed, both bam and bai files are located in the same folder. 

I am unable to figure out the problem. I will really appreciate if you can point out what am I missing.

 

Thank you,

 

Khushbu Patel

Bioinformatics Scientist I

Maris Lab | Department of Biomedical and Health Informatics (DBHi)

The Children’s Hospital of Philadelphia

3501 Civic Center Blvd, Philadelphia, PA 19104

Contact: pate...@email.chop.edu