LUMPY.vcf missing contig info in the header

[arnikz]

bcftools raises warnings:

[W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '2' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '4' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '5' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '6' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '8' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '9' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '10' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '11' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '12' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '13' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '14' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '15' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '16' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '18' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '19' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '21' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '22' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'X' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'Y' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'MT' is not defined in the header. (Quick workaround: index the file with tabix.)

A quick fix:

awk '{printf "##contig=<ID=%s,length=%s>\n", $1, $2}' catalog.fa.fai > contigs.txt

Related issue: arq5x/lumpy-sv#211