diff --git a/README.md b/README.md index df628a4b..d945f0b8 100644 --- a/README.md +++ b/README.md @@ -184,9 +184,8 @@ according to the sequence divergence. Due to a design flaw, BAM does not work with CIGAR strings with >65535 operations (SAM and CRAM work). However, for ultra-long nanopore reads minimap2 may align ~1% of read bases with long CIGARs beyond the capability of BAM. If -you convert such SAM/CRAM to BAM, recent samtools will throw an error and -abort. Older samtools and other tools may even silently create corrupted and -unreadable BAMs. +you convert such SAM/CRAM to BAM, Picard and recent samtools will throw an +error and abort. Older samtools and other tools may create corrupted BAM. To avoid this issue, you can add option `-L` at the minimap2 command line. This option moves a long CIGAR to the `CG` tag and leaves a fully clipped CIGAR @@ -197,7 +196,7 @@ htsjdk, bedtools2, Rsamtools and igv.js. If they are accepted, future versions of these tools will seamlessly recognize long-cigar records generated by option `-L`. -In summary, if you work with ultra-long reads and use tools that only process +**TD;DR**: if you work with ultra-long reads and use tools that only process BAM files, please add option `-L`. #### The cs optional tag