Hi All,
When BWA aligns a read that spans over two chromosomes, it sets the flag as "unmapped" but leaves mapping quality (MAPQ) and CIGAR unchanged.
Picard's validator tool ValidateSamFile throws a validation error for such reads because it expects an unmapped read to have MAPQ of zero, and CIGAR value of "*".
I would like to understand the generally acceptable way of handling this type of reads. Should I modify these reads to have MAPQ 0 and CIGAR value of * ?
I would appreciate any suggestions and best practices to follow for such reads.
Thanks in advance.
When BWA aligns a read that spans over two chromosomes, it sets the flag as "unmapped" but leaves mapping quality (MAPQ) and CIGAR unchanged.
Picard's validator tool ValidateSamFile throws a validation error for such reads because it expects an unmapped read to have MAPQ of zero, and CIGAR value of "*".
I would like to understand the generally acceptable way of handling this type of reads. Should I modify these reads to have MAPQ 0 and CIGAR value of * ?
I would appreciate any suggestions and best practices to follow for such reads.
Thanks in advance.
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