Closed cjw85 closed 1 year ago
Yes. We are investigating how whatshap implemented this.
@cjw85 The release version v1.0 can output haplotype-tagging reads via haplotag
. Sufficient multithreads are better for speed. 8 threads: ~31 min. 16 threads: ~16 min. 32 threads: ~11 minutes.
longphase_linux-x64 haplotag -s snp.vcf -b alignment.bam -t 32
Very often after phasing variants its useful to create a BAM file with reads tagged as to which haplotype they belong, as in the
whatshap haplotag
command. Running this tagging as a discrete process involves additional IO; would it be possible to add BAM read tagging as an additional feature to longphase?