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Proposed enhancement to the FAQ with a line for -M #198

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Proposed enhancement to the FAQ with a line for -M #198

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Update README.md
mdkeehan May 9, 2018
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Merge pull request #1 from mdkeehan/mdkeehan-patch-1
mdkeehan May 9, 2018
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5 changes: 5 additions & 0 deletions README.md
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Expand Up @@ -80,6 +80,7 @@ do not have plan to submit it to a peer-reviewed journal in the near future.
5. [How can a BWA-backtrack alignment stands out of the end of a chromosome?](#endref)
6. [Does BWA work with ALT contigs in the GRCh38 release?](#altctg)
7. [Can I just run BWA-MEM against GRCh38+ALT without post-processing?](#postalt)
8. [When should I use the -M option?](#minusM)

#### <a name="type"></a>1. What types of data does BWA work with?

Expand Down Expand Up @@ -160,6 +161,10 @@ post-processing helps to reduce false mappings caused by reads from the
diverged part of ALT contigs and also enables HLA typing. It is recommended to
run the post-processing script.

#### <a name="minusM"></a>8. When should I use the -M option ?

The BWA MEM -M option was implemented to generate alignments backwardly compatible to SAM versions prior to X.Y .
Picard had not been updated to implement the changes to the SAM specification. Picard has caught up with the SAM specification since Picard version U.V.W. from around 2015


[1]: http://en.wikipedia.org/wiki/GNU_General_Public_License
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