Parallel xargs by Chr

This applet slices a BAM file by canonical chromosome then performs a parallelized samtools view -c using xargs. Type man xargs for general usage information.

View full source code on GitHub

How is the SAMtools dependency provided?

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

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

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

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

/usr/bin is part of the $PATH variable, so the script can reference the samtools command directly, for example, samtools view -c ....

Parallel Run

Splice BAM

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

To split a BAM by regions, you need 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, you generate the *.bai in the applet, sorting the BAM if necessary.

# Download BAM from DNAnexus
dx download "${mappings_bam}"

# Attempt to index the BAM file
indexsuccess=true
bam_filename="${mappings_bam_name}"
samtools index "${mappings_bam_name}" || indexsuccess=false

# If indexing fails, sort then index
if [[ $indexsuccess == false ]]; then
  samtools sort -o "${mappings_bam_name}" "${mappings_bam_name}"
  samtools index "${mappings_bam_name}"
  bam_filename="${mappings_bam_name}"
fi

# Extract chromosome names from header
chromosomes=$(
  samtools view -H "${bam_filename}" | \
  grep "@SQ" | \
  awk -F '\t' '{print $2}' | \
  awk -F ':' '{
    if ($2 ~ /^chr[0-9XYM]+$|^[0-9XYM]/) {
      print $2
    }
  }'
)

# Split BAM by chromosome and record filenames
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 Splice BAM, you recorded the name of each sliced BAM file into a record file. Next, perform a samtools view -c on each slice using the record file as input.

In the following example, $view_options represents any optional additional flags you want to pass to samtools view.

counts_txt_name="${mappings_bam_prefix}_count.txt"

# Sum all read counts across split BAM files
sum_reads=$(
  < bamfiles.txt xargs -I {} \
  samtools view -c $view_options '{}' | \
  awk '{s += $1} END {print s}'
)

# Write the total read count to a file
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