SAM file validation errors after running gencore

[luederm]

Hello,

After deduplicating with gencore I am getting a number of errors with GATK's ValidateSamFile:

• ERROR::MISMATCH_MATE_ALIGNMENT_START, Mate alignment does not match alignment start of mate
• ERROR::MISMATCH_FLAG_MATE_NEG_STRAND, Mate negative strand flag does not match read negative strand flag of mate
• ERROR::MATES_ARE_SAME_END, Both mates are marked as first of pair
• ERROR::MISMATCH_FLAG_MATE_UNMAPPED, Mate unmapped flag does not match read unmapped flag of mate
• ERROR::MATE_NOT_FOUND, Mate not found for paired read

I don't get these errors when I run ValidateSamFile on the BAM file pre-deduplication.