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Old 01-10-2016, 12:08 PM   #1
stanedav
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Location: Czech rep.

Join Date: Jan 2016
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Default Denovogear - unable to find trio

Hello, I am trying denovogear for trio analysis, I started with three .bam files (f1.bam, f2.bam and f3.bam).
First I made bcf file:
samtools mpileup -gDf hg19.fa f1.bam f2.bam f3.bam > output.bcf

then I used my bcf in denovo gear:

./denovogear dnm auto --ped pedfile.ped --bcf output.bcf

PED file:
fam1 f1.bam f2.bam f3.bam 2 1

and I am getting this error:
Unable to find trio. Code 3:3
BCF PARSING ERROR - Trios! -3
Exiting !

Any ideas what I'm doing wrong?

Thanks for your advice

D.
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