How to filter delly variants?

Question

[gt]

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.

Answer 1

[trausch]

Bcftools 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