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whatshap haplotag and split for polyploid #408
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it's previous command as: "variants.vcf" was based on FreeBayes with illumina, and "aln.best.sort.bam" from HIFI data mapping. Thank you. |
I never participated in the haplotag command, but there was supposed to be a polyploid version of it at some point. I think it's still hidden in the |
Polyploid haplotagging would be super useful! 1++ for this feature. |
Closing this, as the feature has been implemented in the meantime. |
Hi, I am using whatshap to analyze polyploid data, and when I run 'whatshap haplotag', I find that it can't handle polyploid data, there is no "--ploidy" parameter. The results of haplotag are shown as diploids (H1, H2 and none) in resule "haplotypes.tsv".
Any ideas on how to fix for polyploid?
the command as:
whatshap haplotag -o haplotagged.bam --reference ref.fa phased.vcf.gz aln.best.sort.bam --output-threads=5 --ignore-read-groups
--output-haplotag-list haplotypes.tsv
Thank you.
Whatshap version 1.6
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