[BioC] samtools error

Yu Chuan Tai yuchuan at stat.berkeley.edu
Thu May 31 05:57:45 CEST 2012


I tried to convert a SAM file from Bowtie2 output to a BAM file, however, 
it didn't work.

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

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

[main_samview] fail to read the header from "../AlignedData/S1_L001_001.SAM".

When I used Bowtie2, I tried to include SAM headers and not include SAM 
headers, both gave me the same error.
Could anyone tell me what's going on here, since I just started to use 
samtools today.

Yu Chuan

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