Haplotag offers the option --cram to output CRAM format. By default, it outputs BAM format.
Currently, phase combines different alignments of the same read into a single alignment. Additionally, a new parameter -L, --overlapThreshold=[0~1] is added to filter out different alignments of the same read if there is overlap.
Summary
@PGtag to the header.--cramto output CRAM format. By default, it outputs BAM format.phasecombines different alignments of the same read into a single alignment. Additionally, a new parameter-L, --overlapThreshold=[0~1]is added to filter out different alignments of the same read if there is overlap.Changes
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