BAM filtering query - ok to have multiple primary alignments in BAM file?

[lucygarner]

Hi,

In your paper, you say that you "discard those reads with low alignment quality, including MAPQ < 20, aligned length < 30 nt and FLAG with UNMAP, SECONDARY, QCFAIL (and DUP if UMI is not applicable)."

I am using STAR for mapping and have set the parameter outSAMprimaryFlag as AllBestScore rather than the default OneBestScore. This means that all alignments with the best score are labelled as primary, rather than just one alignment being labelled as primary (and the rest as secondary).

Will this cause problems for cellsnp-lite or is it ok if there are multiple primary alignments?

Best wishes, Lucy