Converting Chimeric.out.sam to Bam

[Ron]

Hi Alex,

I want to convert the Chimeric.out.sam file to bam file to view the fusion evidence.
here is my code:

samtools view -bS {1} | \
samtools sort - -@ 4 {1/.}.sorted ; \
samtools-0.1.19/samtools index {1/.}.sorted.bam

I am getting the following error:

[bam_header_read] EOF marker is absent. The input is probably truncated.
[samopen] SAM header is present: 25 sequences.

Any suggestions ?

Thanks,

Ron

[Alexander Dobin]

Hi Ron,

I think the warning message is because of the piping of the "view" commands into the "sort" command, since the BAM file from "view" is not fully written when "sort" accesses it. I think the command may work fine despite the message, however, I think it's safer to run without piping.

Cheers

Alex

[Dario Strbenac]

You should upgrade to samtools version 1.4. The version you're using, 0.1, is very out of date.