sambamba-view error with pacbio SAM files

biod / sambamba

Tools for working with SAM/BAM data

http://thebird.nl/blog/D_Dragon.html

GNU General Public License v2.0

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Closed elcortegano closed 4 years ago

elcortegano commented 4 years ago

I am trying to produce BAM files from pacbio SAM files aligned with NGMLR. When I run:

sambamba view -f bam -o file.bam file.sam

I got the following error:

sambamba-view: Error reading BGZF block starting from offset 0: wrong BGZF magic

What is wrong with this? samtools view works fine over the same file.

pjotrp commented 4 years ago

The BAM file is not bgzf encoded.