samtools depth does not output positions with zero coverage

[mfoll]

This means that the estimated coverage can be biased, as the zeros are not counted when calculating the mean/median coverage? samtools depth now offers an option (-a) to resolve this so it should be straightforward:
samtools/samtools#374

[slzhao]

Thanks, Matthieu! Added it.

Best,
Shilin

2016-05-04 7:03 GMT-05:00 Matthieu Foll notifications@github.com:

This means that the estimated coverage can be biased, as the zeros are not
counted when calculating the mean/median coverage? samtools depth now
offers an option (-a) to resolve this so it should be straightforward:
samtools/samtools#374 samtools/samtools#374

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#5

[mfoll]

Great thanks, will try it and let you know.