How to filter delly variants?
1 answer
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
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