Standardize outputs for DELLY and Manta?

[WuSelina]

Hello!
I am wondering if it is possible to have the outputs from DELLY and Manta match, as in both be in binary (BCF) or not (VCF). Right now, it looks like DELLY outputs are in binary.

I am also wondering if the information outputted by Manta's four compressed VCFs is contained in the one DELLY BCF output.
To confirm, do the Manta outputs only contain somatic SVs?
Thank you so much for your help.

[Faizal-Eeman]

Thanks Selina,
Issue #98 created to compress Manta VCF outputs to BCF.

I am also wondering if the information outputted by Manta's four compressed VCFs is contained in the one DELLY BCF output. To confirm, do the Manta outputs only contain somatic SVs?

For somatic SV calling, you'd consider somaticSV.vcf.gz from the Manta output as SVs and indels are scored under a somatic variant model. See this Manta doc for description of each VCF output. The other VCFs appear to have unfiltered variant calls. So, variants called in somaticSV.vcf.gz from Manta may also be called in the DELLY BCF output.

[WuSelina]

Thanks Faizal! Do you think it's better to output both Manta and DELLY outputs as BCFs or VCFs?

[Faizal-Eeman]

BCFs would be better as they are compressed, so lesser file size.