Structural Variation Discovery: Delly's Output

Question

[novice]

I have a question about Delly's MAPQ value. Before calling SVs on my data, I filtered all reads with MAPQ 20 or less. In Delly's output, however, many of the SV predictions have MAPQ values less than 20. So my question is how does Delly calculate MAPQ score?

Thanks.

Answer 1

[trausch]

For SV discovery, delly uses MAPQ and filters reads with MAPQ < q where q is by default 1.

For SV genotyping, delly hashes the mapping qualities of both pairs and uses the minimum of these 2 mapping qualities as the paired-end quality. For bwa alignments it uses the AS tag (alignment score) instead of MAPQ because that worked better in genotyping benchmarks.