Duplicate entries in Pindel output

[stevekm]

I was having problems with the annotation of the .vcf output from Pindel, due to the presence of duplicate entries in the .vcf. For example:

#CHROM | POS | ID | REF | ALT | QUAL | FILTER | INFO | FORMAT | NORMAL | TUMOR

chr2 | 113983582 | . | T | TGGGAGTCCGGGGCCAGGAGGGACAGAGGAGTCAGTATTCTGTATTTTCAACGCCCCCCACCCGGACGGGTGGGAGGGT | . | PASS | END=113983582;HOMLEN=0;SVLEN=78;SVTYPE=INS | GT:AD | 0/0:1083,1 | 0/0:1115,0

chr2 | 113983582 | . | T | TGGGAGTCCGGGGCCAGGAGGGACAGAGGAGTCAGTATTCTGTATTTTCAACGCCCCCCACCCGGACGGGTGGGAGGGT | . | PASS | END=113983582;HOMLEN=0;SVLEN=78;SVTYPE=INS | GT:AD | 0/0:1083,1 | 0/0:1115,0

There are many such entries in the .vcf file produced.

I thought this might an issue with the .vcf conversion from the original data format, but the duplicates actually appear inside the raw data output as well:

$ grep 113983582 pindel_output/*
pindel_output/_SI:530	I 78	NT 78 "GGGAGTCCGGGGCCAGGAGGGACAGAGGAGTCAGTATTCTGTATTTTCAACGCCCCCCACCCGGACGGGTGGGAGGGT"	ChrID chr2	BP 113983582	113983583	BP_range 113983581	113983583	Supports 1	1	+ 1	1	- 0	0	S1 2	SUM_MS 60	2	NumSupSamples 1	1	NORMAL 1083 1071 1 1 0 0	TUMOR 1115 1105 0 0 0 0
pindel_output/_SI:552	I 78	NT 78 "GGGAGTCCGGGGCCAGGAGGGACAGAGGAGTCAGTATTCTGTATTTTCAACGCCCCCCACCCGGACGGGTGGGAGGGT"	ChrID chr2	BP 113983582	113983583	BP_range 113983581	113983583	Supports 1	1	+ 1	1	- 0	0	S1 2	SUM_MS 60	2	NumSupSamples 1	1	NORMAL 1083 1071 1 1 0 0	TUMOR 1115 1105 0 0 0 0

Why are duplicate entries being reported? And is it safe to remove them? What is the recommended removal method?

I am using Pindel version 0.2.5b9