How can I filter delly output to only deletions and ones that PASSED the quality check? I want to use the delly output from delly call.
[Bcftools][1] works best for filtering VCF/BCF files. For instance

`bcftools query -f '%CHROM\t%POS\t%INFO/END\t%ID\t%INFO/SVTYPE\t%QUAL\t%FILTER\n' delly.bcf`

generates a table with all the information you want. Alternatively, you can also filter the VCF/BCF directly using:

`bcftools view -i 'FILTER="PASS" & INFO/SVTYPE="DEL"' delly.bcf`


  [1]: http://samtools.github.io/bcftools/