[Vcftools-help] Intersecting SNPs with vcftools vcf-isec - error message

[Rebecca W. <We...@ca...>]

Hi,

I would like to identify all of the intersecting SNPs in .vcf files generated from snippy (https://github.com/tseemann/snippy). There are 71 .vcf files that were generated from mapping reads onto a P. aeruginosa PA14 reference genome. I am trying to use vcftools vcf-isec to identify the intersecting snps. The .vcf files have been compressed by bgzip and indexed by tabix to give .vcf.gz and .vcf.gz.tbi files.

When I run vcf-isec on just two of the files as a test I get the following error message:

$ vcf-isec -n +2 1_snps.vcf.gz 2_snps.vcf.gz | bgzip -c > isec.vcf.gz



Leading or trailing space in attr_key-attr_value pairs is discouraged:

        [Description] [Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' ]

        INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' ">

 at /usr/share/perl5/Vcf.pm line 180.

If I run vcf-validator on one of the files I get the following error message:

$ vcf-validator 1_snps.vcf.gz



Leading or trailing space in attr_key-attr_value pairs is discouraged:

        [Description] [Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' ]

        INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' ">

However I can run a check on the file before it is compressed with bgzip and it works with the following output:

$ vcftools --vcf 1_snps.vcf



VCFtools - v0.1.13

(C) Adam Auton and Anthony Marcketta 2009

Parameters as interpreted:

        --vcf Tsb_1_snps.vcf

After filtering, kept 1 out of 1 Individuals

After filtering, kept 40 out of a possible 40 Sites

Run Time = 0.00 seconds

Please do you have any suggestions about the error messages I am getting with vcf-isec or vcf-validator? Any help would be appreciated.

Thanks.

Beky