bgzf_read error during samtools run
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6.6 years ago
kk.mahsa ▴ 140

hi

when i used following command on my bam file:

samtools view -F 4 myfile.bam | perl -lane 'print "$F[2]\t$F[3]"' > 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.

software error samtools cnv-seq bgzf • 3.7k views
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Entering edit mode
6.6 years ago

Somehow your BAM file got corrupted. You'll want to remake it.

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