Picard ValidateSamFile error
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!
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Pierre Lindenbaum
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boyu93 •
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boyu93 •
1 answer
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.
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