vcf-consensus outputs <DEL> in the FASTA file instead of simply deleting the ref allele. (Previously reported by Albert Gevorgyan on the vcftools-help mailing list).
This patch fixes the issue:
--- vcf-consensus 2014-03-26 15:40:25.000000000 +0000 +++ vcf-consensus-jh 2014-06-09 14:11:59.000000000 +0100 @@ -176,6 +176,11 @@ if ( !defined $alt ) { return; } } + if ($alt eq "<DEL>" or $alt eq "-") + { + $alt = ""; + } + if ( $$vline[1] <= $$opts{fa_frz} ) { print STDERR "Note: Conflicting variants at (or near) $$vline[0]:$$vline[1], cannot apply both.\n";
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This patch fixes the issue: