VCF Failing Validations

Im hitting some issues with validating VCFs from CRISP with GATK and VCFtools validators. This seems to be a simple whitespace issue.

[12:36][cfljam@aklbld31:PoolSeq (master)] $ vcf-validator ./CRISP/CHR26.CRISP.vcf.gz
The column QUAL is empty at CHR26:253.
Wrong number of fieldsin ./CRISP/CHR26.CRISP.vcf.gz; expected 13, got 14. The offending line was:
[CHR26  253     .       A       G               0       PASS    NP=4;DP=65,34;VT=SNV;CT=0.0;QVpf=-48.4;QVpr=-18.9;VP=4;MQ=0,0,0,101       GT:AF:ADf:ADr   0/0:0.467:10,8:6,6      0/0:0.375:8,6:7,3       0/0:0.345:13,8:6,2      0/0:0.500:5,7:3,1]

 at /software/bioinformatics/vcftools-0.1.14/share/perl5/Vcf.pm line 172, <__ANONIO__> line 19.
        Vcf::throw('Vcf4_0=HASH(0x2295d60)', 'Wrong number of fieldsin ./CRISP/CHR26.CRISP.vcf.gz; expected...') called at /software/bioinformatics/vcftools-0.1.14/share/perl5/Vcf.pm line 505

This appears to be simple matter of a double tab between ALT and QUAL fields.


zcat ./CRISP/CHR1.CRISP.vcf.gz | grep -v "^##" | cat -t | head -n 3
#CHROM^IPOS^IID^IREF^IALT^IQUAL^IFILTER^IINFO^IFORMAT^Ialign/pool1.merged.dedup.relign.RG.bam^Ialign/pool2.merged.dedup.relign.RG.bam^Ialign/pool3.merged.dedup.relign.RG.bam^Ialign/pool4.merged.dedup.relign.RG.bam
CHR1^I24^I.^IG^IA^I^I12^IPASS^INP=4;DP=75,77;VT=SNV;CT=-1.3;QVpf=-26.4;QVpr=-22.5;VP=4;MQ=1,1,3,151^IGT:AF:ADf:ADr^I0/0:0.157:26,3:17,5^I0/0:0.286:10,5:10,3^I0/0:0.385:8,9:16,6^I0/0:0.147:12,2:17,3
CHR1^I45^I.^IG^IA^I^I19^IPASS^INP=4;DP=74,91;VT=SNV;CT=-2.0;QVpf=-36.1;QVpr=-19.5;VP=3;MQ=1,1,2,167^IGT:AF:ADf:ADr^I0/0:0.375:19,10:16,11^I0/0:0.222:7,5:14,1^I0/0:0.229:13,7:24,4^I0/0:0.059:11,2:21,0

vibansal / crisp

VCF Failing Validations #2