run SVDetect on one sample

[jazberna1]

Hi,

This is not an issue. I just wanted to ask you if SVDetect cnv could be potentially run with one sample only by setting the mates_file_ref option to the normal reads bam file of the same sample, something like in the configuration file below.

Any help will be much appreciated.

Jorge

<general>
input_format=bam
sv_type=all
mates_orientation=FR
read1_length=90
read2_length=90
mates_file=sample.sorted.ab.bam
cmap_file=hg38.chr.lengths
output_dir=/svdetect_output
tmp_dir=/svdetect_output/tmp
num_threads=12
</general>

<detection>
split_mate_file=1
window_size=30000
step_length=10000
mates_file_ref=sample.sorted.norm.bam
</detection>