An error when I used vcfutils vcf2fq

Question

[jinzheng9406]

I try to use vcfutils convert a vcf file which have been process by bcftools view.

But when I run the commond 'vcfutils vcf2fq xxx.vcf > xxx.fq', there is a error.

substr outside of string at /usr/local/bin/vcfutils.pl line 557, <> line 81277. Use of uninitialized value in lc at /usr/local/bin/vcfutils.pl line 557, <> line 81277. substr outside of string at /usr/local/bin/vcfutils.pl line 557, <> line 81277.

Did someone meet the same error? How to solve it?

Thank you!

Answer 1

[baorong2018]

Hello, I meet the same error. substr outside of string at /nas/longleaf/apps/samtools/1.8/bin/vcfutils.pl line 557, <> line 15851640. Use of uninitialized value in lc at /nas/longleaf/apps/samtools/1.8/bin/vcfutils.pl line 557, <> line 15851640. substr outside of string at /nas/longleaf/apps/samtools/1.8/bin/vcfutils.pl line 557, <> line 15851640.

Would you like to tell me how to solve it?

Thank you!