[svtoolkit-help] A question about GenomeSTRiP

[Jaemin K. <jm...@sn...>]

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?
 

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 9349869 24 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
 

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