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Old 12-21-2012, 12:11 PM   #1
ihelbig
Junior Member
 
Location: Kiel, Germany

Join Date: Dec 2012
Posts: 3
Default Where is the denovogear output?

Dear all,
I am trying to use DeNovoGear for DNM in trios and have used mpileup using the following command
samtools mpileup -gDf hg19.fasta A1096.bam A1097.bam A1098.bam > trio1.bcf
This gave me a "Segmentation fault: 11", but I decided to move on with DeNovoGear using
"denovogear dnm auto --ped trio1.ped --bcf trio1.bcf"
The program finished after 10 min with "Done!", but I don't see any output or error message?
I am using Mac OS 10.7.5 with DeNovoGear 0.5.1-3-gde06767.

Could anyone tell me whether this is a samtools issue or denovogear issue
Best wishes,
Ingo
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