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Search: Posts Made By: fitzgeraldlm
Forum: Bioinformatics 02-03-2011, 10:59 AM
Replies: 3
Views: 2,358
Posted By fitzgeraldlm
Hi Libiyagirl, I'm pretty sure you use this...

Hi Libiyagirl,

I'm pretty sure you use this command in Stage 3 of Dindel, although I didn't end up trying it. I ended up teaching myself how to use GATK and have successfully done a local...
Forum: Bioinformatics 01-20-2011, 03:04 PM
Replies: 3
Views: 2,358
Posted By fitzgeraldlm
Dindel --outputRealignedBAM

Has anyone tried using the --outputRealignedBAM option in Dindel?

I would like to try using the realigned BAM files Dindel outputs in SAMtools for SNV calling but I can't work out where to use...
Forum: Bioinformatics 01-08-2011, 02:01 PM
Replies: 9
Views: 3,776
Posted By fitzgeraldlm
Solved

A big thank you to gaffa and skblazer. I have now got Stage 4 running and have a VCF file! Thanks for the tip on how to create the txt file gaffa. I did have to add the whole path name, like you...
Forum: Bioinformatics 01-07-2011, 03:45 PM
Replies: 9
Views: 3,776
Posted By fitzgeraldlm
Unhappy Dindel Stage 4 problems

Hi,

I'm having similar problems to Lien, however mine are unfortunately not solved yet :( I'm not sure if I understand your solution skblazer or the original instructions (very new to unix/linux)....
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