Re: [Samtools-help] samtools do not validate uncompressed BAM file

[Heng Li <lh...@sa...>]

I guess that "BAM" is actually a bgzip compressed SAM, not really a BAM. Samtools would not work on a BAM decompressed by "bgzip -d". You can try "samtools view -SH" on that file to see what you get.

Heng

On Sep 29, 2011, at 4:35 PM, Soboleva, Alexandra (NIH/NLM) [E] wrote:

> Dear samtools developers,
> 
> We encountered the following problem.
> 
> We received uncompressed BAM file as a part of submission to GEO database
> 
> When we tried to validate it with "samtools view -H", there was error message
> 
> [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 "GSM721162_1b.bam".
> 
> After I compressed file with bgzip, I was able to read its header.
> According to documentation, samtools are able to read input file either
> compressed or uncompressed.
> 
> 
> samtools versions tried: 0.1.15 and 0.1.18
> 
> 
> Thanks for looking into it!
> 
> 
> Alexandra Soboleva
> GEO group software developer lead
> NCBI/NLM/NIH
> 
> 
> 
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