Jasmine doesn't work with Smoove

[teresa1997]

Hello! I'm using Jasmine to merge vcf files obtained from different tools of the same sample. Those are the tools that I'm currently using: Manta, Delly, Whamg, Svaba and Smoove. I can merge all the tools without problems except for smoove. When I put smoove with the others, Jasmine can merge but smoove ramains always as a single call even if there are variants in common. I tried to merge smoove aginst itself (with another sample) and it's working. I also tried to merge Smoove against each one of the other tool and it's not working. Those are the parameter that I'm using:

jasmine
file_list=ID.tool.txt
out_file=ID.vcf
genome_file=Homo_sapiens_assembly38.fasta
bam_list=ID.bam.txt
max_dist_linear=1.0
threads=16
min_overlap=0.75
min_support=2
--ignore_type
--normalize_type

The INFO field of each VCF is a little bit different but still, the others can be merged together. If you want I can send you the different vcf via email.

[mkirsche]

Hi,

Thanks for your interest in using Jasmine! From looking at the Whamg sample VCFs on their Github repo, it looks like their SV calls include the STRANDS INFO field, while other callers such as Delly do not use it as far as I know. This could cause issues with merging between these callers since by default Jasmine only matches variants with the same value in this field, so I would recommend adding the --ignore_strand command line flag when running Jasmine. If that doesn't work it would be very helpful if you could share some of the VCFs (the Whamg one and at least one other) or samples from them so I could try to replicate the problem.

Best, Melanie

[teresa1997]

I tried with the --ignore_strand parameter and now it's working. Thank you for your kindness Melanie!!!

[mkirsche]

No problem - I'm glad that helped!!

Melanie