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Run tricolor on our simulated data #8

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wdecoster opened this issue Oct 11, 2021 · 2 comments
Open

Run tricolor on our simulated data #8

wdecoster opened this issue Oct 11, 2021 · 2 comments

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@wdecoster
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@DamarisLa
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DamarisLa commented Oct 11, 2021 •
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https://davidebolo1993.github.io/tricolordoc/usecases/usecases.html

#with haplotype-resolved BAM
TRiCoLOR SENSoR -bam <HAPLOTYPE1.BAM> <HAPLOTYPE2.BAM> -o

#with haplotype-tagged BAM
TRiCoLOR SENSoR -bam <HAPLOTAGGED.BAM> -o

==> output bedfile

#TRiCoLOR REFER --help

#with haplotype-resolved BAM
TRiCoLOR REFER -g <REFERENCE.FASTA> -bam <HAPLOTYPE1.BAM> <HAPLOTYPE2.BAM> -bed <REPETITIONS.BED> -o

#with haplotype-tagged BAM
TRiCoLOR REFER -g <REFERENCE.FASTA> -bam <HAPLOTAGGED.BAM> -bed <REPETITIONS.BED> -o

==> output VCF and bedfile

@lfpaulin
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lfpaulin commented Oct 13, 2021 •
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See tricolor-analysis/human in dnanexus and tricolor-analysis/tomato (pending upload)

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@wdecoster @lfpaulin @DamarisLa