I found some problematic VCF files created by Lifescope software. The sequencing was done on Solid 5500. These VCFs cannot be merged with other VCF files. The variants in these files are all indels. When I run vcf-validator it seems the "-" in the allele is the problem. Some vcf-validator output:
[lifescope@scyld small.indel]$ perl -I/home/lifescope/bin/vcftools_0.1.11/perl /home/lifescope/bin/vcftools_0.1.11/bin/vcf-validator 37_1_3/2013_08_13_exome_high.gff3.vcf
Warning: The file is not sorted, for example chr12:53690189 comes after chr12:53690191
chr12:53690189 .. Could not parse the allele(s) [-]
[lifescope@scyld small.indel]$ perl -I/home/lifescope/bin/vcftools_0.1.11/perl /home/lifescope/bin/vcftools_0.1.11/bin/vcf-validator 37_1_4/2013_08_13_exome_high.gff3.vcf
Warning: The file is not sorted, for example chr11:108100105 comes after chr11:108100112
chr11:108100105 .. Expected combination of A,C,G,T,N for REF, got [-], the offending chars were [-]
Does any other Lifescope user have the same problem? Is there an easy way to fix this? Thank you in advance!
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