​ View full source code on GitHub​

How is the SAMtools dependency provided?

The SAMtools compiled binary is placed directory in the <applet dir>/resources directory. Any files found in the resources/ directory will be uploaded so that they will be present in the root directory of the worker. In our case:

├── Applet dir
│   ├── src
│   ├── dxapp.json
│   ├── resources
│       ├── usr
│           ├── bin
│               ├── < samtools binary >

When this applet is run on a worker, the resources/ folder will be placed in the worker’s root directory /:

/
├── usr
│   ├── bin
│       ├── < samtools binary >
├── home
│   ├── dnanexus

/usr/bin is part of the $PATH variable, so in our script, we can reference the samtools command directly, as in samtools view -c ...

Parallel Run

Splice BAM

First, we download our BAM file and slice it by canonical chromosome, writing the *bam file names to another file.

In order to split a BAM by regions, we need to have a *.bai index. You can either create an app(let) which takes the *.bai as an input or generate a *.bai in the applet. In this tutorial, we generate the *.bai in the applet, sorting the BAM if necessary.

  dx download "${mappings_bam}"
​
  indexsuccess=true
  bam_filename="${mappings_bam_name}"
  samtools index "${mappings_bam_name}" || indexsuccess=false
  if [[ $indexsuccess == false ]]; then
    samtools sort -o "${mappings_bam_name}" "${mappings_bam_name}"
    samtools index "${mappings_bam_name}"
    bam_filename="${mappings_bam_name}"
  fi
​
​
  chromosomes=$(samtools view -H "${bam_filename}" | grep "\@SQ" | awk -F '\t' '{print $2}' | awk -F ':' '{if ($2 ~ /^chr[0-9XYM]+$|^[0-9XYM]/) {print $2}}')
​
  for chr in $chromosomes; do
    samtools view -b "${bam_filename}" "${chr}" -o "bam_${chr}."bam
    echo "bam_${chr}.bam"
  done > bamfiles.txt

Xargs SAMtools view

In the previous section, we recorded the name of each sliced BAM file into a record file. Now we will perform a samtools view -c on each slice using the record file as input.

  counts_txt_name="${mappings_bam_prefix}_count.txt"
​
  sum_reads=$(<bamfiles.txt xargs -I {} samtools view -c $view_options '{}' | awk '{s+=$1} END {print s}')
  echo "Total Count: ${sum_reads}" > "${counts_txt_name}"

Upload results

The results file is uploaded using the standard bash process:

1. Upload a file to the job execution’s container.

2. Provide the DNAnexus link as a job’s output using the script dx-jobutil-add-output <output name>

     counts_txt_id=$(dx upload "${counts_txt_name}" --brief)
     dx-jobutil-add-output counts_txt "${counts_txt_id}" --class=file