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Old 11-27-2014, 10:51 AM   #1
hbl_ca
Junior Member
 
Location: canada

Join Date: Apr 2013
Posts: 1
Default 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.
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