![]() We recommend the workflow included below for diagnosing problems with ValidateSamFile. Fortunately there's a handy Picard tool that can test for (almost) all possible SAM/BAM format errors, called ValidateSamFile. To fix these problems, you first have to know what's wrong. The source of these errors is usually introduced by upstream processing tools, such as the genome mapper/aligner or any other data processing tools you may have applied before feeding the data to Picard or GATK. ![]() In addition, the SAM/BAM index file can be a source of errors as well. Invalid SAM/BAM files generally have one or more errors in the following sections: the header tags, the alignment fields, or the optional alignment tags. This means that there is something wrong either with the content of the file (something important is missing) or with its format (something is written the wrong way). The most frequent cause of these unexplained problems is not a bug in the program - it's an invalid or malformed SAM/BAM file. Bits of the stack trace (the pile of lines in the output log that the program outputs when there is a problem) may contain the following:, Error Type Count, NullPointerException - or maybe something else that doesn't mean anything to you. ![]() You're trying to run a GATK or Picard tool that operates on a SAM or BAM file, and getting some cryptic error that doesn't clearly tell you what's wrong.
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