Problem for pindel2vcf to create VCF file from pindel created _D files

Question

[hongbing.li]

Hi

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'
what(): basic_string::erase
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.

[Pierre Lindenbaum]

chr1 is ~250E6 bp but your tool is trying to read 300E6 bp ? did you write a config file with this '300000000' ?

[nnutter]

This was cross-posted on SEQanswers.

[liangkaiye]

Can you communicate with me by email on this? [e-mail]

I need the pindel output lines causing the error.

[hongbing.li]

Thanks for your remind .

[steven_friedenberg]

Hi there, I am having a similar problem with pindel2vcf. Here is my command:

/path/to/pindel2vcf -p /path/to/pindel_chrXsubset_D -r /path/to/canFam3.fa -R canFam31 -d 20141204 -v /path/to/pindel_chrXsubset_D.vcf -G

And the output I'm getting is:

terminate called after throwing an instance of 'std::out_of_range'
  what():  basic_string::erase

Thanks for any thoughts you might have.

Steve

[hongbing.li]

Problem has been resolved by Lingkaiye.

Thanks for all of you!

[winnie]

Hi.

I experience the same sort of problem. Could you post about how to fix it please?

/winnie

My Error message:

Exiting reference scanning.
Processing chromosome P0116_N055-10_trimmed_(paired)_contig_1_consensus
Reading region 0-300000000
Reading chromosome P0116_N055-10_trimmed_(paired)_contig_1_consensus into memory.
terminate called after throwing an instance of 'std::out_of_range'
  what():  basic_string::erase: __pos (which is 60) > this->size() (which is 3)
Abort trap: 6

[hongbing.li]

Hi winnie,

Following is resolved by Liangkeye for me

grep ChrID P2_Index_13_P375_D > P2_Index_13_P375_D.head.txt
../pindel2vcf -p P2_Index_13_P375_D.head.txt -r hg19.fasta -R hg19-GRCh37 -d 200902 -v P2_Index_13_P375_D.head.txt.vcf

[winnie]

I will give a go. Thank you.

best regards,

Winnie

Answer 1

[hongbing.li]

Thanks for all your response, and I have sent files to [e-mail]