Since v 2.1.3, parsnp has handled multi-fasta references a produces a vcf with the correct CHROM labels. It seems like the bed file produced by running PhiPack (--recomb-filter) doesn't support this yet.
11:08 cn4325 clade1$ tail parsnp.rec
1 12308168 12308268 REC 0.000 +
1 12328295 12328395 REC 0.000 +
1 12333736 12333836 REC 0.000 +
1 12337892 12337992 REC 0.000 +
1 12349452 12349552 REC 0.000 +
1 12366020 12366120 REC 0.000 +
1 12379228 12379328 REC 0.000 +
1 12385718 12385818 REC 0.000 +
1 12395554 12395654 REC 0.000 +
1 12404985 12405085 REC 0.000 +
Since v 2.1.3, parsnp has handled multi-fasta references a produces a vcf with the correct CHROM labels. It seems like the bed file produced by running PhiPack (--recomb-filter) doesn't support this yet.