Thank you for the great program.
Before taking further action, I would like to verify a few things.
I have a number of .sorted.bam files from various aligners. Using these bam files, is there any way I could jump into the SVJedi for calling SVs? According to the manual, it says "python3 svjedi.py -v -p ".
Q1: Can I use the bam files for .paf?
Q2: If not, do I need to convert SAM/BAM to PAF using paftools or htsbox (https://www.biostars.org/p/479287/)? If yes, which parameters do I need to consider?
Q3: If the current version is not accepting the BAM file, is there any chance you could consider upgrading it for your next version release?
Hi Lolita,
Thank you for the great program. Before taking further action, I would like to verify a few things. I have a number of .sorted.bam files from various aligners. Using these bam files, is there any way I could jump into the SVJedi for calling SVs? According to the manual, it says "python3 svjedi.py -v -p ".
Q1: Can I use the bam files for .paf? Q2: If not, do I need to convert SAM/BAM to PAF using paftools or htsbox (https://www.biostars.org/p/479287/)? If yes, which parameters do I need to consider? Q3: If the current version is not accepting the BAM file, is there any chance you could consider upgrading it for your next version release?
Looking forward to your reply!
Kind regards,
Taek