Question about VariationHunter!

Question

[meng.zijian]

Hi All,

I am a new user to VariationHunter. I am trying to use it with non-human genome. The output files are empty when I run it. It seems I have to change settings when I run it with non-human genome. Right?

But I don't know how to do it because I don't find the solutions in its manual. Is there anyone who knows how to do it? Any help will be appreciated!

Thank you very much!

Zijian

[Pierre Lindenbaum]

show us the command line.

[meng.zijian]

First, I calculated some basic information about my bam file which is derived from alignment after duplicates Marking. They are: Mean Insert Size: 478.5; Minimum Insert Size is 100; Maximum Insert Size is 121827452. Standard Deviation is 21.6.

Then, I use the "Mean Insert Size- 4Standard Deviation" as the minimum parameter and "Mean Insert Size+4Standard Deviation" as the maximum one to convert the bam file into DIVET format which is input format for VariationHunter.

At last, I run the ./VariationHunter_SC:

Please enter the minimum paired-end insert size: 100
Please enter the maximum paired-end insert size: 121827452
Please enter the pre-processing mapping prune probability: 1
Please enter the minimum support for a cluster: 2

I am learning on NGS. I don't know where the problem is. I also tried other parameters in the command line, like setting a smaller maximum insert size. But it still failed. I think I need to change some settings in order to use the tool with non-human genome. Right? Any help will be appreciated!

Thank you!

[andrew.j.skelton73]

How did you derive mean insert size? - That seems pretty big.