Giuseppe1995

Ok, thanks, I got it... Since I have also copy number data (I'm working on tumor-normal matched samples) I can try to integrate them with the output from SvABA ....

Hi, yes, now I have an answer to all the doubts raised by myself more than one year ago, now. 1) For somatic SV detection, is pretty useless to try...

this is the normal: `samtools view -H $BAM_NORMAL` > @SQ SN:gi|8486122|ref|NC_002016.1| LN:1027 > @SQ SN:gi|8486125|ref|NC_002017.1| LN:1778 > @SQ SN:gi|8486127|ref|NC_002018.1| LN:1413 > @SQ SN:gi|8486129|ref|NC_002019.1| LN:1565 > @SQ SN:gi|8486131|ref|NC_002020.1| LN:890 > @SQ...

Sorry, could you indicate which one is duplicated? Because I checked the bam header of the two files and they appear to be identical, and no contig seems to be...

Yes, it works in every one of my conda env. I hoped I didn't have to create another environment. Is this possible?

Thank you so much! I have solved this problem as follows: I ran the command `cat ${INSTALLATION_DIR}/HiC-Pro-master/check_python.log` that gave me the following output: Traceback (most recent call last): File "/srv/ngs/analysis/dalteriog/Tools/HiC-Pro-master/tmp/../scripts/install/check_pythonlib.py",...

Hi, I've also encountered the same issue, and (in my case) the problem was that some samples had 0 properly paired reads (`samtools flagstat` output). you can find a tread...