Mike Keehan comments

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                                            Mike Keehan

Fix GT splitting in bcftools norm

I think its a fundamental problem with representing multi allelics as binary. Three alleles A,B,C Gives the following genotypes: alleles|A|B|C --------|-|-|- A|A/A|A/B|A/C B| |B/B|**B/C** C| | |C/C If we try...

a small test

This all started with #179

Please enhance documentation on the recommended use of the BWA MEM -M and -Y option

Thinking about it a bit more. It might be that GATK use -M for consistency for non ALT references So currently planning on going ahead without -M. Just in case...

Please enhance documentation on the recommended use of the BWA MEM -M and -Y option

Ok - I'll reopen it. Which file would be best to enhance with documentation explaining the "recommendations for use" of the more subtle options? The Readme.md or the bwa.1 man...

Please enhance documentation on the recommended use of the BWA MEM -M and -Y option

Please see pull request #198

Suggestions

Hi Hao, I have thought about this some more. The third commit 78c5faf013aff27c089bf78daa4cd726bbe4e589 is a large style change and interacts with commit da6d2ee. Parts of 78c5faf may be redundant once...