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5050- [ Usage] ( #usage )
5151 - [ Variant calling with PacBio HiFi/Nanopore long reads] ( #variant-calling-with-pacbio-hifinanopore-long-reads )
5252 - [ Multiple input BAM/CRAM files of the same sample] ( #multiple-input-bamcram-files-of-the-same-sample )
53- - [ Low allele-fraction mosaic variant calling] ( #low-allele-fraction-mosaic-variant-calling )
53+ - [ Low- allele-fraction mosaic variant calling] ( #low-allele-fraction-mosaic-variant-calling )
5454 - [ Region-specific variant calling] ( #region-specific-variant-calling )
5555 - [ Output phased (\& refined) long-read BAM/CRAM] ( #output-phased--refined-long-read-bamcram )
5656 - [ Variant calling from remote files] ( #variant-calling-from-remote-files )
124124longcallD call -t16 ref.fa sample_part1.bam -X sample_part2.bam -X sample_part3.bam > sample.vcf
125125```
126126
127- ### Low allele-fraction mosaic variant calling
128- With ` -s ` , longcallD will detect both germline and low-fraction somatic/mosaic variants.
127+ ### Low- allele-fraction mosaic variant calling
128+ With ` -s ` , longcallD will detect both germline and low-allele- fraction somatic/mosaic variants.
129129
130130For each somatic/mosaic variant, a ` SOMATIC ` tag will be added to the INFO field in the output VCF.
131131```
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