Alternative to Split'N'CigarReads in Galaxy

Question

[srimeenakshi1603]

I would like to use GATK best practice method in Galaxy for identifying SNPs in RNA-seq data. After preprocessing my reads, I want to split and trim the reads using SplitNCigarReads tool. Unfortunately, the particular tool is not available in the Galaxy platform. Is there any alternative tool available to SplitNCigarReads?

[Ram]

Please add a link to the protocol you're following.

[Pierre Lindenbaum]

Is there any alternative tool available to SplitNCigarReads?

better: don't use galaxy and try to use a command-line.

[h.mon]

Duplicate: Alternative tools to SplitNCigarReads