pysam.utils.SamtoolsError cannot parse region "chr22_KI270879v1_alt:267307-281486"

[geocarvalho]

Hello @sbslee, I hope you are well.
I'm trying to run a WGS sample that was run using Dragen 3.9 for the prepare-depth-of-coverage and have the below error:

$ docker run -v "$PWD":/data pypgx:v0.15.0 pypgx prepare-depth-of-coverage /data/sample/sample_WGS-depth-of-coverage.zip /data/sample_WGS/sample_WGS-contigs.bam --assembly GRCh38
ERROR conda.cli.main_run:execute(33): Subprocess for 'conda run ['pypgx', 'prepare-depth-of-coverage', '/data/sample_WGS/sample_WGS-depth-of-coverage.zip', '/data/sample_WGS/sample_WGS-contigs.bam', '--assembly', 'GRCh38']' command failed.  (See above for error)
Traceback (most recent call last):
  File "/opt/conda/envs/myenv/bin/pypgx", line 10, in <module>
    sys.exit(main())
  File "/opt/conda/envs/myenv/lib/python3.8/site-packages/pypgx/__main__.py", line 33, in main
    commands[args.command].main(args)
  File "/opt/conda/envs/myenv/lib/python3.8/site-packages/pypgx/cli/prepare_depth_of_coverage.py", line 90, in main
    archive = utils.prepare_depth_of_coverage(
  File "/opt/conda/envs/myenv/lib/python3.8/site-packages/pypgx/api/utils.py", line 1232, in prepare_depth_of_coverage
    cf = pycov.CovFrame.from_bam(bams, regions=regions, zero=True)
  File "/opt/conda/envs/myenv/lib/python3.8/site-packages/fuc/api/pycov.py", line 261, in from_bam
    results += pysam.depth(*(bams + args + ['-r', region]))
  File "/opt/conda/envs/myenv/lib/python3.8/site-packages/pysam/utils.py", line 69, in __call__
    raise SamtoolsError(
pysam.utils.SamtoolsError: 'samtools returned with error 1: stdout=, stderr=samtools depth: cannot parse region "chr22_KI270879v1_alt:267307-281486"\n'

I think it is happening because the contig name is different:

$ samtools idxstats sample_WGS-contigs.bam | grep chr22
chr22
chr22_KI270731v1_random
chr22_KI270732v1_random
chr22_KI270733v1_random
chr22_KI270734v1_random
chr22_KI270735v1_random
chr22_KI270736v1_random
chr22_KI270737v1_random
chr22_KI270738v1_random
chr22_KI270739v1_random

I have removed the reads in these random contigs because I'm trying to use a sample already aligned instead of aligning it again without the contigs. Do you think there is any other way of solving it? Maybe creating the sample_WGS-depth-of-coverage.zip file out of pypgx?

Thank you.

[sbslee]

@geocarvalho,

This is a GRCh38-specific issue. One of the genes with SV is GSTT1 and it is located in the contig chr22_KI270879v1_alt, which is missing in your BAM file. That's why the prepare-depth-of-coverage command is complaining. For more details, please read GRCh37 vs. GRCh38.

In any case, the solution is to exclude the GSTT1 gene when running the command:

$ pypgx prepare-depth-of-coverage \
depth-of-coverage.zip \
in.bam \
--assembly GRCh38 \
--genes GSTT1 \
--exclude

Please try this.

[geocarvalho]

Thank you @sbslee, it worked. I'll study how to deal with this gene in the future.