I've been trying without luck to use the SplitRead software (http://splitread.sourceforge.net/) published in Karakoc, E. et al. Detection of structural variants and indels within exome data. Nat Meth 9, 176–178 (2012). The version at the sourceforge link (v0.1) had several bugs, but the developer was kind enough to send me a revised version. However I'm still having no luck running the basic pipeline.
Specifically, Step 5 in the basic pipeline (available here) results in two empty output files. I am unsure whether this is due to there being no structural variants in my sample or with a bug in the getSC.sh script.
I've emailed the developer for assistance twice over the past three weeks and had no response. Has anyone successfully run the SplitRead software?
Thanks,
Pete
Specifically, Step 5 in the basic pipeline (available here) results in two empty output files. I am unsure whether this is due to there being no structural variants in my sample or with a bug in the getSC.sh script.
I've emailed the developer for assistance twice over the past three weeks and had no response. Has anyone successfully run the SplitRead software?
Thanks,
Pete
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