5. Output files

-out option allows to specify the output directory or the name for the image file (if a single image file is the output).

5.1. Image file (PNG, JPG)

By default, the program generates image files in png format. It is possible to select jpg format using the -imagetype option.

$ bamsnap \
  -bam ./data/NA12878.bam \
  -pos chr10:117542948 \
  -out ./out/NA12878_chr10_117542948.jpg \
  -imagetype jpg \
  -save_image_only

Note

To save only snap image files, use the -save_image_only option.

Inside the output directory, images are saved in a default sub-directory. It is possible to rename this folder using the the -image_dir_name option.

$ bamsnap \
  -bam ./data/NA12879.bam \
  -vcf ./data/NATRIO_test_3.vcf \
  -out ./out/NATRIO_test_3 \
  -image_dir_name test_images

This example creates ./out/NATRIO_test_3/test_images folder that contains the generated snap image files.

By default, the program generates a single plot file for multiple bam files. -separated_bam option allows to generate a plot file for each of the bam files.

5.2. Compressed file (-zipout)

It is possible to save a compressed (zip) output file using the -zipout option.

$ bamsnap \
  -bam ./data/NA12879.bam \
  -vcf ./data/NATRIO_test_3.vcf \
  -out ./out/NATRIO_test_3 \
  -save_image_only \
  -zipout

This example creates ./out/NATRIO_test_3.zip file.

5.3. HTML file (index html)

If -save_image_only is not used, index.html is generated by default.