[svtoolkit-help] Input to SVAltAlign

[Gayle L. <gay...@de...>]

<font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2">Hi,<br><br>I'm trying to run Genome STRIP on a dataset but the output from the SVDiscovery module (the vcf file) can't be used as input to SVAltAlign. I think this is because the potential variants are tagged as 'imprecise', even though the confidence intervals around the ends are 0 for some events - consequently the alternative allele sequence isn't generated. Is there some way of getting around this? Or should I use some other algorithm such as tigra_sv to process the vcf file?<br><br>If you could help me with this that would be great,<br><br>Gayle <br><div></div></font>