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@twolinin twolinin released this 03 Aug 06:45
· 128 commits to main since this release
v1.5.1
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Learn about vigilant mode.

Release note of v1.5.1
There are two major update in this release.

  1. Multi-bam input is now supported. The user can specify multiple BAM files by
longphase phase \
-s SNP.vcf \
-b alignment1.bam \
-b alignment2.bam \
-r reference.fasta \
-t 8 \
-o phased_prefix \
--ont # or --pb for PacBio Hifi
  1. A beta version of SNP and modification co-phasing is now released. Feedback are very welcome. The user can detect allele-specific modifications (5mC only at this moment) by a new command modcall, assuming the MM/ML tags are carried to aligned BAM.
longphase modcall \
-b alignment.bam \
-r reference.fasta \
-t 8 \
-o modcall

The SNP and modification co-phasing can then be invoked by providing the modcall-generated VCF. Co-phasing SNPs and modifications can further improve the phasing contiguity.

longphase phase \
-s SNP.vcf \
--mod-file modcall.vcf \
-b alignment.bam \
-r reference.fasta \
-t 8 \
-o phased_prefix \
--ont # or --pb for PacBio Hifi
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