Hi, I am trying to call some targeted mutations from multiple targeted regions and chromosomes by Deepvariant. I followed the manual of make_examples.py to separate the multiple regions by space(

), but it showed an error like the following:
sudo docker run -v "${INPUT_DIR}":"/input" -v "${OUTPUT_DIR}:/output" google/deepvariant:"${BIN_VERSION}" /opt/deepvariant/bin/run_deepvariant --model_type=WGS --ref=/input/Homo_sapiens_assembly19.fasta --reads=/input/proper.bam
--regions="3:178936057-178936106 3:178952054-178952106"
--output_vcf=/output/outputch3.vcf.gz --output_gvcf=/output/outputchr3.g.vcf.gz
--num_shards=1 --make_examples_extra_args vsc_min_fraction_snps=0.004
E0416 22:33:24.439428 140413429749504 errors.py:61] Command line parsing failure: make_examples does not accept positional arguments but some are present on the command line: "['/tmp/Bazel.runfiles_xs3AuO/runfiles/com_google_deepvariant/deepvariant/make_examples.py', '3:178952054-178952106']".
I wonder whether this issue is due to the chromosome index of my sample is 1-22 without ‘chr’ and how to run it with multiple regions and multiple chromosomes.

Another issue is that when I changed the region to the bed file which includes all targeted regions, the variants called are all false-positive and none true variants included.

Furthermore, my sample is from deep sequencing on targeted regions. I have followed issue #62 to change the pileup_image_hight and downsample_fraction options, but the results are not improved.

Thanks a lot!
Best regards,
Weiwei