Comments (2)
Hi Roxane,
Thanks for reaching out.
Could you check if there are other reads mapped to the other contigs?
Thanks
Fritz
from sniffles.
Hi Fritz, thanks for your fast answer,
Indeed, reads are also mapped on all other contigs.
I tried to launch again sniffle by using more parameters (First time I only used input and output), and it seems it is still running and it is reading my others contigs as well in the end.
Here the difference between my first and e second command :
#SNiffle try number1
./sniffles -m '/media/loutre/SUZUKII/alignement/ngmlr-pacbio/ngmlr-pacbio-suzukii-sorted.bam' -v '/media/loutre/SUZUKII/break-point-research/sniffles/variant-detection-sniffles.vcf'
#Sniffle with more parameters
./sniffles -m '/media/loutre/SUZUKII/alignement/ngmlr-pacbio/ngmlr-pacbio-suzukii-sorted.bam' -v '/media/loutre/SUZUKII/break-point-research/sniffles/variant-detection-sniffles2.vcf' --cluster --genotype --cluster_support 10 -l 1000
from sniffles.
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