Tool:Variationhunter

Question

[Malachi Griffith]

VariationHunter is a package of programs used to find structural variations using paired-end reads read mappings.

VariationHunter-SC

Maximum Parsimony based Structural variation.

Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes

[meng.zijian]

Hi Malachi,

I am learning to use the tool. It seems to be created to solve problems in human genome, but I think the method should be used in other species which is next generation data. Is that right?

If so, do I need to change some settings when I run this tool? I tried to run it, but there are several errors which I don't find solutions to solve it.

First, I use a script to convert my bam file after the realignment into DIVET format which is the input of VariationHunter. To convert the bam file, I set up the "Mean Insert Size-4*Standard Deviation" as the minimum parameter and "Mean Insert Size+4*Standard Deviation" as the maximum parameter. After that, I got the DIVET format file. Then I run ./VariationHunter_SC with the result for minimum insert size and maximum insert size calculated from Picard with my bam file. In addition, I set up "1" for pre-processing mapping prune probability and "2" for minimum support for a cluster. But the problem is that the final SV.DElETION result file is empty. So are others. In addition, there is an error in screen which is "Segment Fault" under the Chr 22. Only chr 21 has results.

If I use only Chr2 in my input file, the error won't be listed in the screen, but the result file is still empty. Is there something wrong with my setting or do I need to change some setting when I run the tool for non-human species?

Any help will be appreciated! Thank you very much!