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FelixKrueger / Bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states
http://felixkrueger.github.io/Bismark/
GNU General Public License v3.0
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Bismark bam format #156

Closed josesovaz closed 6 years ago

josesovaz commented 6 years ago

Dear Felix,

I write this issue to ask you if the bam file created with Bismark has the same "universal bam" format As I read in the manual, I think is a little bit different. If not, I would want to ask you if there is the possibility to convert the Bismark bam like any genomic bam file (even manually).

Thank you in advance,

Regards,

Jose

FelixKrueger commented 6 years ago

Hi Jose,

The Bismark BAM file should adhere to the standard BAM conventions. It does have a few optional fields to accommodate the bisulfite specific features, and it required some tweaking of the FLAG values to fit standard BAM FLAGS (because Bisulfite-Seq can have 4 different strands as opposed to just 2 strands in conventional sequencing). But the bottom line is: it should behave pretty much like any other BAM file.

josesovaz commented 6 years ago

Perfect. Thank you very much for your answer.

Regards,

Jose