Picard ValidateSamFile error

Question

[boyu93]

I wanted to run Breakdancer but received an error EOF marker is absent. So I tried Picard ValidateSamFile to see if there are any errors inside. When I run Picard ValidateSamFile, I received the following error:

ValidateSamFile Value for tag MC is not a String: class java.lang.Integer

I couldn't find any useful information on it, could anybody help me with the issue? Thanks a lot!

Answer 1

[Pierre Lindenbaum]

EOF marker is absent

you'd better try to re-generate the bam. There is a problem with the file.

MC = "CIGAR string for mate/next segment" should be encoded in your bam as a string ( see https://samtools.github.io/hts-specs/SAMtags.pdf )

MC:X:50M

but it's encoded in your bam as an interger

MC:i:50M

it's a problem with the software that created the BAM.

[boyu93]

Thank you so much! We found out that it was caused during copying into the disk, the file is not complete with only first several chromosomes included. I'd better check the completeness first in the future.