Re: [svtoolkit-help] A question about GenomeSTRiP

[Bob H. <han...@br...>]

On 4/6/12 2:32 AM, Jaemin Kim wrote:
>
> Hello, Steven McCarroll
>
> I'm Jaemin Kim, a graduate student in Seoul National University. I'm 
> trying to identify the CNV of horse and pig NGS via GenomeSTrip, but 
> I'm having some difficulties.
>
> 1.Can you please send me an README file or the description file of the 
> output format? I tested with small sets, but I don't know how to 
> interpret the result file (For example, the first column denotes for 
> this, the second for this, and so on). Do you have the explanation of 
> the final output files in output directory?
>
The final output files are in vcf format: 
http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
I think they are compatible with v4.1, but if you find discrepancies, 
please let me know.
>
> 2.Also, during the SV Discovery Process, I see the following message; 
> java.lang.IllegalArgumentException: *Left read of read pair fails left 
> read test*: HWI-ST840:150:C097JACXX:1:1101:12655:134832 145 29 
> 934986924 4M1I94M 29 9349874-92 
> GATCTCGTGGCATAGTGGTTGGGTTCAGCATCCTCTGCTTTGGTGCCCCAGGTTTGCAGGTTCAGATCCTGGGCATGGATCTACACCACTTGTCAGCCA 
> DDBD@@DCDDDDDDDDDDDDBDEEDEEDFDFFFHHHGGJIIJIJIJJIHIJJIJIJJIJJJJJJJJIJIIJIGBIIIJGHFIFGCIGFHHHGFFFFFBB 
> MD:Z:1C0C95 RG:Z:P00033F1.001 XG:i:1 NM:i:3 XM:i:2 XN:i:0 XO:i:1 
> MQ:i:24 AS:i:-18 YS:i:-20 YT:Z:DP
>
There should have been two "#DBG:" lines directly before this error - 
can you send them?
Thanks,
-Bob
>
> Can you please tell me how to fix this error? We used the test samples 
> of 7.
>
> I really think that this is a useful tool, considering the population 
> basis. So could you please help me on these questions? I will really 
> appreciate your consideration.
>
> Sincerely,
>
> Jaemin Kim
>
>
>
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