search

samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
Other
654 stars 240 forks source link

norm split multiallelic error #290

Closed dwaggott closed 9 years ago

dwaggott commented 9 years ago

It only happens when I use -m -, ideas?

bcftools norm -f GRCh37.fa -m - test.vcf > test2.vcf

bcftools: vcfnorm.c:385: split_info_numeric: Assertion `ret==src->n_allele-1' failed.
Aborted

test.vcf

pd3 commented 9 years ago

The VCF has incorrect number of AO fields, the tag is defined as Number=A, but fewer values are present. The vcf-validator complains: 1:10177 .. FORMAT tag [AO] expected different number of values (expected 2, found 1)

dwaggott commented 9 years ago

Thanks, I'll file a ticket with the tool.

Is the vcf-validator available for use?

Beyond malformed, I'm regularly running into files where a single row is truncated.

pd3 commented 9 years ago

Latest htslib versions check for missing eof gbzf block (https://github.com/samtools/htslib/commit/58358e1514a1d7317a5f8296c1837685a19a467d), the file has to be compressed for this.

The vcf-validator comes with the vcftools package (https://github.com/vcftools/vcftools/blob/master/perl/vcf-validator).