---
title: 'samtools flagstat'
output:
    html_document:
      number_sections: true
      toc: true
      theme: cosmo
      highlight: tango
---

```{r setup, include=FALSE, warning=FALSE, message=FALSE}
knitr::opts_chunk$set(
  echo = ECHO
)
```


# Code for computational analysis

```{r 'run flagstat'}
command = paste0('samtools flagstat ', opt$input_bam, ' > report.txt')
system(command)
```