Anyone got SplitRead software to work?

[PeteH]

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

[pepsimax]

I've tried to use it as well, but I can't even get the first stage to work. When I run "./SplitReadAll_lite ..." I get a seg fault. Do you know if the revised version that you got has since been uploaded to sourceforge, or is it still the old one? It still says V0.1, so I guess it's not been updated. In that case, could I get it off you as I've had no reply from the designer either. I'd really appreciate it!

[PeteH]

I've tried to use it as well, but I can't even get the first stage to work. When I run "./SplitReadAll_lite ..." I get a seg fault. Do you know if the revised version that you got has since been uploaded to sourceforge, or is it still the old one? It still says V0.1, so I guess it's not been updated. In that case, could I get it off you as I've had no reply from the designer either. I'd really appreciate it!

That's the same error I encountered with v0.1. I can send you the version the author sent me (private message me your email address), however I have not been able to run this version to completion either. I've given up on it - it shouldn't be up to the users to fix such fundamental problems with the software.
Pete

[vishal.rossi]

Hi Pete,

Can you send me the version which the author sent you? I am messaging my email address.

Thanks in Advance
Regards
Vishal

[lintao]

Hi Pete,

Recently, I used splitread softwar, I also encountered some difficulties wih you previously. Can you please send me the version that you think it is OK? I am messaging my email address.

I greatly appreciate your help!

Thank you!

lintao

[lintao]

Hi Pete,

Recently, I used splitread softwar, I also encountered some difficulties wih you previously. Can you please send me the version that you think it is OK? I am messaging my email address.

I greatly appreciate your help!

Thank you!

lintao

[PeteH]

Hi Pete,

Recently, I used splitread softwar, I also encountered some difficulties wih you previously. Can you please send me the version that you think it is OK? I am messaging my email address.

I greatly appreciate your help!

Thank you!

lintao

Hi Lintao,

I didn't receive your private message. Nevertheless, I should make it clear that the version of the software that I was sent still does not work.

Cheers,
pete