I'm trying to convert an aligned bam file (produced by the genomics
platform at the Broad) to a fastq file in order to perform alignment
against a custom genome. I get the error below. Do the fastq files
contain all the reads, except the ones for which a mate was not found?
Thanks.
Exception in thread "main" htsjdk.samtools.SAMFormatException: SAM
validation error: ERROR: Found 13 unpaired mates
at htsjdk.samtools.SAMUtils.processValidationError(SAMUtils.java:465)
at picard.sam.SamToFastq.doWork(SamToFastq.java:192)
at
picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:183)
at picard.sam.SamToFastq.main(SamToFastq.java:137)
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