Problem with read IDs repeated in the same BAM file

[gymreklab]

We get the following error if there is more than one read pair in a given region with the same read ID:

"ERROR: Failed to extract passes filters tag from BAM alignment"

These reads were from supplementary alignments. Ignoring alignments marked as supplementary would likely solve this issue. This is similar to a previous issue when read ids were repeated across BAM files (rather than within).

CC @shubhamsaini

[tfwillems]

@gymreklab @shubhamsaini
Could you send me a BAM file that on its own can reproduce this issue?

[gymreklab]

Using HipSTR version v.0.6.1

./HipSTR/HipSTR --version
HipSTR version v0.6.1

Attached files for the command below
chr9.testregions.bed.zip
hipstr_error_reads.bam.zip

Command:

HipSTR \
    --bams hipstr_error_reads.bam \
    --fasta /storage/resources/dbase/human/GRCh38/GRCh38_full_analysis_set_plus_decoy_hla.fa \
    --regions chr9.testregions.bed \
    --output-gls \
    --min-reads 1 \
    --def-stutter-model \
    --str-vcf test.vcf.gz

[kkapuria3]

I am getting the same error,

"ERROR: Failed to extract passes filters tag from BAM alignment"

I don't even know the reason why. I have 136 samples, how do I know which one is busted ?

[shadrinams]

Any updates / recommendations on the error? Thank you.

[douym]

We get the following error if there is more than one read pair in a given region with the same read ID:

"ERROR: Failed to extract passes filters tag from BAM alignment"

These reads were from supplementary alignments. Ignoring alignments marked as supplementary would likely solve this issue. This is similar to a previous issue when read ids were repeated across BAM files (rather than within).

CC @shubhamsaini

same problem here. To "ignore alignments marked as supplementary", do we need to change the bam file or is there a parameter for HipSTR to do that? THX

[CyrusWang57]

For me, this error was not caused by a supplementary read. When I removed supplementary reads from my bam file, the error was still there. I don't know what caused the error, even after checking reads reported the error (they look all fine). But I simply modified the source code to skip this error. The following steps are for your reference.

1. Locate the passes_filters function in the bam_processor.cpp source file.
2. Modify the function as the provided changes.

void BamProcessor::passes_filters(BamAlignment& aln, std::vector<bool>& region_passes) {
    assert(region_passes.empty());
    std::string passes;
    if (!aln.GetStringTag("PF", passes)) {
        // PF tag not found, add a new one with value "0"
        passes = "0";
        if (!aln.AddStringTag("PF", passes)) {
            printErrorAndDie("Failed to add PF tag with value '0' to BAM alignment");
        }
        std::cout << "Added PF tag with value '0' to alignment" << std::endl;
    }
    for (int i = 0; i < passes.size(); i++) {
        region_passes.push_back(passes[i] == '1' ? true : false);
    }
}

3. Recompile the project to implement the changes through command ‘make’.

This process should address the problem.