VCF output

Pindel outputs a VCF file based on the VCFv4.1 spec, it adds the following custom fields.

VCF Block	NAME	Details
INFO	PC	Pindel call
INFO	RS	Range start
INFO	RE	Range end
INFO	LEN	Length
INFO	REP	Change repeat count within range
INFO	S1	S1
INFO	S2	S2
INFO	FF017	Variant must not overlap with a simple repeat
FORMAT	FC	Fragment calls
FORMAT	FD	Fragment depth
FORMAT	GT	Genotype
FORMAT	NB	BWA calls on the negative strand
FORMAT	ND	BWA mapped reads on the negative strand
FORMAT	NP	Pindel calls on the negative strand
FORMAT	NR	Total mapped reads on the negative strand
FORMAT	NU	Unique calls on the negative strand
FORMAT	PB	BWA calls on the positive strand
FORMAT	PD	BWA mapped reads on the positive strand
FORMAT	PP	Pindel calls on the positive strand
FORMAT	PR	Total mapped reads on the positive strand
FORMAT	PU	Unique calls on the positive strand