I am new pindel user, and use ../pindel -f hg19.fasta -i p1_config.txt -c ALL -o P2_Index_95_P319 to create P2_Index_95_P319 with _SI, _D, and so on. When I use pindel2vcf to create vcf file with _SI. I got it. and also found some interesting insertion. But when I create vcf filw with_D, using "../pindel2vcf -p P2_Index_95_P319_D -r hg19.fasta -R hg19-GRCh37 -d 200902 -v P2_Index_95_P319_D.vcf" , some error is as following:
Exiting reference scanning.
Processing chromosome chr1
Reading region 0-300000000
Reading chromosome chr1 into memory.
terminate called after throwing an instance of 'std::out_of_range'
Aborted (core dumped)
It will be appreciated to give suggestion from anybody. I try other samples, All _SI get its vcf, but _D gives same errors.