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docs/output.md

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-[NGSCheckMate](https://github.com/parklab/NGSCheckMate) is a tool to verify that samples come from the same individual, by examining a set of single nucleotide polymorphisms (SNPs). This calculates correlations between the samples, and then applies a depth-dependent model of allele fractions to call samples as being related or not. The principal output is a dendrogram, where samples that are .
+[NGSCheckMate](https://github.com/parklab/NGSCheckMate) is a tool to verify that samples come from the same individual, by examining a set of single nucleotide polymorphisms (SNPs). This calculates correlations between the samples, and then applies a depth-dependent model of allele fractions to call samples as being related or not. The principal outputs are a dendrogram, where samples that are considered to match are shown as connected, a matrix showing the correlations between each samples, and a text file detailing each match between files.
 This requires a bed file specifying the SNPs to consider to be provided as input. The NGSCheckMate github provides such sets of bed files for hg19 and hg38 that have been selected as being typically heterogeneous across the population and are present in exonic regions. The tool can also be used to verify samples match between different sequencing modalities, for instance matching RNA-Seq with ATAC-seq, ChIP-seq and WGS.
 
 ## Pseudoalignment and quantification