when i used following command on my bam file:
samtools view -F 4 myfile.bam | perl -lane 'print "$F\t$F"' > myfile.hits
i got this message:
[E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes
[main_samview] truncated file.
anybody can help me to resolve it.