Some SNV genome variants were found outside of --target_bed file with --bait_padding

[sitems]

Description of the bug

Relevant portion of my --target_bed file looks like

chr1 35720 35736
chr1 69088 69970
chr1 138529 139696

I'm processing WES fastq file with '--target_bed and --bait_padding 500' options, but in outpur/call_snv/genome/output_snv.vcf.gz I see variants like this

chr1 88177 chr1_88177_G_C G C 8 . AF=1;AQ=8;FOUND_IN=deepvariant GT:DP:AD:GQ:PL:RNC 1/1:2:0,2:6:8,6,0:..

The variant is outside of any (padded) bed region.

Command used and terminal output

No response

Relevant files

No response

System information

No response

[ramprasadn]

Thanks for reporting this sitems! I am working on a fix here #633

[jemten]

Have a new issue with running DeepVariant on exomes after the merge of PR #633.

***** Running the command:*****
time seq 0 35 | parallel -q --halt 2 --line-buffer /opt/deepvariant/bin/make_examples --mode calling --ref "grch37_homo_sapiens_-d5-.fasta" --reads "ADM997A2_sorted_md.bam" --examples "tmp/[email protected]" --channels "insert_size" --gvcf "tmp/[email protected]" --regions "home_bait.intervals_list" --task {}

I1017 19:10:23.285372 139672540231488 genomics_reader.py:222] Reading ADM997A2_sorted_md.bam with NativeSamReader
I1017 19:10:23.315367 139672540231488 make_examples_core.py:301] Task 3/36: Preparing inputs
I1017 19:10:23.389680 139672540231488 genomics_reader.py:222] Reading ADM997A2_sorted_md.bam with NativeSamReader
I1017 19:10:23.405181 139672540231488 make_examples_core.py:301] Task 3/36: Common contigs are ['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '20', '21', '22', 'X', 'Y', 'MT']
Traceback (most recent call last):
  File "/home/proj/stage/analysis/cases/cleanshrimp/work/Bazel.runfiles_ikroupyj/runfiles/com_google_deepvariant/deepvariant/make_examples.py", line 234, in <module>
    app.run(main)
  File "/home/proj/stage/analysis/cases/cleanshrimp/work/Bazel.runfiles_ikroupyj/runfiles/absl_py/absl/app.py", line 312, in run
    _run_main(main, args)
  File "/home/proj/stage/analysis/cases/cleanshrimp/work/Bazel.runfiles_ikroupyj/runfiles/absl_py/absl/app.py", line 258, in _run_main
    sys.exit(main(argv))
  File "/home/proj/stage/analysis/cases/cleanshrimp/work/Bazel.runfiles_ikroupyj/runfiles/com_google_deepvariant/deepvariant/make_examples.py", line 224, in main
    make_examples_core.make_examples_runner(options)
  File "/home/proj/stage/analysis/cases/cleanshrimp/work/Bazel.runfiles_ikroupyj/runfiles/com_google_deepvariant/deepvariant/make_examples_core.py", line 2739, in make_examples_runner
    regions, calling_regions = processing_regions_from_options(options)
  File "/home/proj/stage/analysis/cases/cleanshrimp/work/Bazel.runfiles_ikroupyj/runfiles/com_google_deepvariant/deepvariant/make_examples_core.py", line 2641, in processing_regions_from_options
    calling_regions = build_calling_regions(
  File "/home/proj/stage/analysis/cases/cleanshrimp/work/Bazel.runfiles_ikroupyj/runfiles/com_google_deepvariant/deepvariant/make_examples_core.py", line 607, in build_calling_regions
    ranges.RangeSet.from_regions(regions_to_include, contig_dict)
  File "/home/proj/stage/analysis/cases/cleanshrimp/work/Bazel.runfiles_ikroupyj/runfiles/com_google_deepvariant/third_party/nucleus/util/ranges.py", line 170, in from_regions
    return cls(ranges=from_regions(regions, contig_map=contig_map))
  File "/home/proj/stage/analysis/cases/cleanshrimp/work/Bazel.runfiles_ikroupyj/runfiles/com_google_deepvariant/third_party/nucleus/util/ranges.py", line 117, in __init__
    for i, range_ in enumerate(ranges):
  File "/home/proj/stage/analysis/cases/cleanshrimp/work/Bazel.runfiles_ikroupyj/runfiles/com_google_deepvariant/third_party/nucleus/util/ranges.py", line 509, in from_regions
    yield parse_literal(region, contig_map)
  File "/home/proj/stage/analysis/cases/cleanshrimp/work/Bazel.runfiles_ikroupyj/runfiles/com_google_deepvariant/third_party/nucleus/util/ranges.py", line 597, in parse_literal
    raise ValueError(
ValueError: Could not parse "home_bait.intervals_list" as a region literal.  Region literals should have the form "chr:start-stop" or "chr:start" or just "chr".  A common error is to use the "chr" prefix on inputs that don't have it, or vice-versa.

Looks like the call regions should be defined using bed file format and not interval_list format. Running the deepvariant help command:

--regions: Optional. Space-separated list of regions we want to process. Elements can be region literals (e.g., chr20:10-20) or paths to BED/BEDPE files.

What do you think about using the bed file supplied with the parameter --target_bed instead?