I don’t know what kind of files samtools view –hX out.bam>out.sam and merged SAM are.

Last updated:2014.10.27.

Merged.sam is likely to be the files within the framework of “Download merged pileup file” from the Detail view screen, but this is the results of sam per chromosome, combined into one.
out.samX

samtools view -hX
Usage: samtools view [options]|[region1 [...]]
Options: -h     print header for the SAM output
            -X     output FLAG in string (samtools-C specific) 

For sam and samX, the 2nd column inscription changes. Please refer to the below.

http://sourceforge.net/apps/mediawiki/samtools/index.php?title=SAM_FAQ#The_integer_FLAG_field_is_not_friendly_to_eyes

Merged SAM, if there is one chromosome, has the same contents as out.sam (but the Download files are compressed).

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