NM tag

[Simon White]

I notice that the NM tag in STARs bam files is written as nM. This causes problems when running ATLAS2 for variant calling. Is there a reason the tag is written in this way? If not, would it be possible to change it so it is all uppercase? 

Simon

[Alexander Dobin]

Hi Simon,

the nM tag is different from the standard NM:  nM is simply the number of mismatches per pair (not per mate!), and it does not include the indels (i.e. it's not edit distance).

Calculating the proper NM value is on my TODO list fo rthe next release. Hopefully, ATLAS2 can re-calculate this number for each mate.

Cheers

Alex

[Simon White]

Hi Alex,

Ok - that makes sense. Whilst we are talking TODO lists :) If you could add a MD tag too (String for mismatching positions.) that would be most appreciated.

Cheers,

Simon

[Daniel Fernandez]

Hi Alex,  I also need the MD field for my research, do you have an estimate as to when the MD field could be added to the sam output?  Please let us know if there are plans regarding this, it'd help me a lot.

Thanks!

[Alexander Dobin]

Hi Daniel,

I am so hopelessly behind my schedule that I cannot make a very concrete promise. I hope to release a patch with NM and MD tags in October.

Cheers

Alex

[Daniel Fernandez]

Great, thanks a lot Alex!

[Daniel Fernandez]

Hi akex, have you released or plan to release the NM/MD fields?  No pressure just wondering what's the status of such updates.

Thanks!

On Tuesday, September 24, 2013 1:42:36 PM UTC-4, Alexander Dobin wrote:

[Alexander Dobin]

Hi Daniel,

I am planning to release this a several more features this week. Thanks for your patience.

Cheers

Alex

[Daniel Fernandez]

That sounds great, thanks alex.

[Daniel Fernandez]

Hi Alex, I was wondering, have you released the new features?  if not, any estimate on the release date?  Again, no pressure at all, just wondering.

Happy holidays!

Daniel

[Alexander Dobin]

Hi Daniel,

the NM and MD tags are implemented! 

Please try it out:

ftp://ftp2.cshl.edu/gingeraslab/tracks/STARrelease/Alpha/STAR_2.3.1v.tgz

You need to specify all the attributes you want, for example:

--outSAMattributes NH HI NM MD

The NM and MD tags follow samtools conventions, i.e. they are eaxactly the same as produced by 'samtools fillmd'

I have not tested it very thoroughly, please let me know whether it works for you.

Happy Holidays!

Alex

[Daniel Fernandez]

Great, thanks a lot!

[ShengLin Mei]

Hi,  Alex

The link for STAR_2.3.1 is broken, can you send me a link for the new version. I need NM tag information of mapped reads. 

Best Wishes

Shenglin Mei

在 2013年12月21日星期六UTC-5上午8时20分05秒，Alexander Dobin写道：

[Alexander Dobin]

Hi Shenglin,

our ftp isdown, IT is working on it.

In the meantime you can get the latest release from GitHub:

https://github.com/alexdobin/STAR/releases/tag/ENCODE_2014-03-16_2.3.1z1 

Cheers

Alex