Samtools for corrupt bam?

I am getting an error message with regards to a corrupt bam:


Error: BAM file is corrupt. Samtools cannot parse header

Does anyone know if there is a fix? Or do I have to realign the bam file?

samtools

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written 6.7 years ago by vctrm67 9

Can you try to get the header only? samtools -H file.bam

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written 6.7 years ago by Asaf 1.0K

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