It seems that for some variants (predominantly RPLs) pindel2vcf records the wrong END-value (which subsequently GATK complains about "ERROR MESSAGE: BUG: GenomeLoc 9:17427298-17427314 has a size == 18 but the variation reference allele has length 17") e.g.

chr9  17427298        .       TAGATTTTTCAGCAATAC      AGATTTTTCAGCAATACA      .       PASS    END=17427314;HOMLEN=0;NTLEN=18;SVLEN=-18;SVTYPE=RPL     GT:AD   0/0:0,4

The variant starts at 17427298 and affect a stretch of 18nt (ref allele) so the end should be 17427298+18-1=17427315 not 17427314.

Why does this occur?

In the meantime: this python snippet will correct the END values

import sys
filename=sys.argv[1]
outfile=open(sys.argv[2],"w")

countall=0
count=0 

for i in open(filename):
    if i.find("#")>-1:
        outfile.write(i)
    else:
        countall+=1
        content=i.split("\t")
        start=int(content[1])
        end=int(i.split("END=")[1].split(";")[0])
        length=len(content[3])
        if (start+length-1!=end):
            count+=1
            #print "update length %i %i : %s" % (start+length-1, end, i)
            content[7]=content[7].replace("END="+str(end), "END="+str(start+length-1))
        outfile.write("\t".join(content))

print "%i updated out of %i" % (count, countall)