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.
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.