-v, --invert          Invert filter, return variants that fail at least one criterion
-p, --pass-only       Only retain variants with FILTER of PASS or .
--require-svtype      Only retain variants with SVTYPE INFO field
--require-svlen       Only retain variants with SVLEN INFO field
-l N, --min-svlen N   Minimum |SVLEN| for variants with SVLEN INFO field

# Return PASS SVs at least 50 bp long.
# SVs like BND that do not have an SVLEN attribute are considered to satisfy "--min-svlen"
svpack filter --pass-only --min-svlen 50 A.vcf```

# Return PASS SVs shorter than 50 bp.  Chain two svpack filter commands since if
# "--invert", "--pass-only", and "--min-svlen 50" were specified together then svpack
# would return SVs that do not satisfy either "--pass-only" or "--min-svlen".
svpack filter --pass-only A.vcf | svpack filter --invert --min-svlen 50

-v, --invert              Invert match, return variants in A that do not match a
                          variant in B
-i INFO, --info INFO      Output all records and annotate with INFO field(s)
                          from best match in B. Overrides -v.
-p N, --max-pos-diff N    Maximum difference in POS to consider variants to match [100]
-l N, --max-svlen-diff N  Maximum difference in SVLEN to consider variants to match [100]

# Identify variants in A.vcf that are also seen in B.vcf
svpack match A.vcf B.vcf

# Identify variants in A.vcf that are not seen in B.vcf
svpack match -v A.vcf B.vcf

# Identify variants in KID.vcf that are not seen in MOM.vcf or DAD.vcf
svpack match -v KID.vcf MOM.vcf | svpack match -v - DAD.vcf

# Add the BCSQ tag to A.vcf.  The annotated VCF is written to stdout.
svpack consequence A.vcf ensembl.gff3.gz