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  • Problem for pindel2vcf to create vcf from from pindel-created _D files

    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:ut_of_range'
    what(): basic_string::erase
    Aborted (core dumped)

    I try other samples, All _SI get its vcf, but all of _D give same errors.

  • #2
    This was cross-posted on BioStars.

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