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Table 1 Comparison between mInDel with other InDel calling tools

From: mInDel: a high-throughput and efficient pipeline for genome-wide InDel marker development

Method mInDel SAMtools GATK Atlas2
De novo assembly Yes No No No
Reference genome-independent Yes No No No
Different aligners for different read lengths Yes No No No
InDel sized called Short, Long Short Short Short
High-throughput genotyping compatibility Yes Yes Yes Yes
PCR/electrophoresis genotyping amiability High Low Low Low