In reading the BWA manual, I have come across a question that I still cannot answer. It reads:
So BWA will rescue mates presumably if there is a high-quality, uniquely mapping mate pair. My question is: what are the parameters that the unmapped mate have to meet to be considered correctly placed? For instance, if I have 2x100 reads, and one maps uniquely, does the other one have to map with the same stringency as I specified in the aln stage. Or if say, only 30nt of the unmapped read map, and the other 70nt do not (due to say, an inversion), will the unmapped read be mapped and the 70 non-mapping nucleotides just be soft-clipped in the BAM file?
Any help would be greatly appreciated.
Cheers,
Kevin
In paired-end alignment, BWA pairs all hits it found. It further performs Smith-Waterman alignment for unmapped reads with mates mapped to rescue mapped mates, and for high-quality anomalous pairs to fix potential alignment errors.
Any help would be greatly appreciated.
Cheers,
Kevin
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