BWA bin boundaries disagree with bowtie bin boundaries

robertaboukhalil / ginkgo

Cloud-based single-cell copy-number variation analysis tool

qb.cshl.edu/ginkgo

BSD 2-Clause "Simplified" License

47 stars 28 forks source link

BWA bin boundaries disagree with bowtie bin boundaries #6

Closed mschatz closed 7 years ago

mschatz commented 7 years ago

The BWA bins are determined by finding perfect matches (using a grep for NM:i:0) but doesnt confirm that the alignment is unique. Should check H0 and/or MQ to confirm uniqueness.

robertaboukhalil commented 7 years ago

Is mapping quality >= 30 a good threshold? See pull request #7

mschatz commented 7 years ago

Yes, looks good!

robertaboukhalil commented 7 years ago

Merged!