SOLID and SOCS

[ssharma]

Hi All,
I am using SOCS to map my SOLID reads to a reference genome.
But i am not sure how to use the alignment file generated by SOCS.
Is there any program or s/w to view the alignment file generated by SOCS or how to get coverage information or other useful details.

Thanks
ssharma

[colindaven]

If you get SAM/BAM output you can read on this forum or google as to how to take analysis further.

Else, try a conversion tool, or may I suggest a different aligner such as Bioscope or BWA?