Comparing SvABA running result with ICGC StSM somatic.sv.vcf file

[biotech25]

Hi,

I downloaded tumor and normal BAM files of ICGC donor ID, "DO48701" from ICGC. The tumor BAM file ID is FI44968, and normal BAM file ID is FI44967. I ran SvABA on the BAM files, and got "svaba.unfiltered.germline.sv.vcf (541 vcf calls)" and "svaba.unfiltered.somatic.sv.vcf (789 vcf calls)" Here is my command line;

svaba run -t 6abba3f621d5442ad1e893d1ea11e9c6.bam
-n 1ddf1b0c325527318767571b8b076e13.bam
bwa index ./Homo_sapiens.GRCh37.75.dna.primary_assembly.fa
-G ./Homo_sapiens.GRCh37.75.dna.primary_assembly.fa
-p 16 -D ./DBSNP_knownIndel/dbsnp_indel.vcf
-a DO48701

Question1. Bunt, "svaba.germline.sv.vcf" and "svaba.somatic.sv.vcf" files are empty. This means that all vcf calls were filtered out as they are low quality.. am I correct?

Question2. I downloaded "00c27940-c623-11e3-bf01-24c6515278c0.broad-snowman-10.20151218.germline.sv.vcf" file from ICGC. This file is also from the same donor ID, "DO48701". As you see the file name, it is analyzed by 'snowman'. I compared the vcf callings between this file and "svaba.unfiltered.germline.sv.vcf (541 vcf calls)". But, I couldn't see any common vcf callings. I expected my SvABA running result and ICCC StSM somatic.sv.vcf file show similar performance. Could you advise what I did wrong..?

Thank you, Sanghoon