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There's not. If you want the output in pileup format, then you can just filter things with awk. If you're calling SNPs (i.e., outputting BCF) then you can just filter calls according to per-sample depth once you have things in VCF. -
samtools mpileup min depth option?
Is there an option to output a minimum depth of coverage? I know there is one for maximum depth.
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Innovations in next-generation sequencing technologies and techniques are driving more precise and comprehensive exploration of complex biological systems. Current advancements include improved accessibility for long-read sequencing and significant progress in single-cell and 3D genomics. This article explores some of the most impactful developments in the field over the past year.
Long-Read Sequencing
Long-read sequencing has seen remarkable advancements,...12-02-2024, 01:49 PM
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