zzh
/
minimap2
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

minor wording changes

This commit is contained in:
Heng Li 2017-10-21 23:46:36 -04:00
parent dc37aee881
commit c6b6392b70
1 changed files with 3 additions and 4 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

7
README.md
View File

@ -184,9 +184,8 @@ according to the sequence divergence.
Due to a design flaw, BAM does not work with CIGAR strings with >65535 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 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 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 you convert such SAM/CRAM to BAM, Picard and recent samtools will throw an
abort. Older samtools and other tools may even silently create corrupted and error and abort. Older samtools and other tools may create corrupted BAM.
unreadable BAMs.
To avoid this issue, you can add option `-L` at the minimap2 command line. 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 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 of these tools will seamlessly recognize long-cigar records generated by option
`-L`. `-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`. BAM files, please add option `-L`.
#### <a name="cs"></a>The cs optional tag #### <a name="cs"></a>The cs optional tag