Error: The average coverage of the sample is too low

[rrdavis77]

I have a set of 4 exomes and running aldy 4.4 on them as so:

aldy genotype -g cyp2e1 -p wxs ${bam_location}/*/${sample_name}.bam -o ${output}/${sample_name}.cyp2d6.aldy -l ${output}/${sample_name}.cyp2e1.aldylog

for 3 out of the 4 exomes I am getting errors about the The average coverage of the sample is too low

[main] arguments= subparser=genotype verbosity=INFO file=/home/ryan/NGS_Data/Exome_9-14-23/dragen_analysis/CYP-028/CYP-028.bam gene=cyp2e1 profile=wxs reference=None genome=None cn_neutral_region=None output=/home/ryan/NGS_Data/Exome_9-14-23/vcf/haplotype_aldy4_results_June_2023/CYP-028.CYP2E1.aldy solver=any debug=None cn=None log=/home/ryan/NGS_Data/Exome_9-14-23/vcf/haplotype_aldy4_results_June_2023/CYP-028.CYP2E1.aldylog multiple_warn_level=1 simple=False param=None Genotyping sample CYP-028.bam... WARNING: Copy-number calling is not available for exome data. WARNING: Aldy will NOT be able to detect gene duplications, deletions and fusions. WARNING: Calling of alleles that are defined by non-exonic mutations is not available. Results might not be biologically relevant! [genotype] gene=cyp2e1; start=2023-09-27 18:52:17.572901 [lp] solver= cbc [genotype] reference= hg19 [params] neutral_value=786.0; cn_parsimony=1.0; min_coverage=5.0 [sam] path= /home/ryan/NGS_Data/Exome_9-14-23/dragen_analysis/CYP-028/CYP-028.bam [sam] Read SAM took 1.22s [coverage] scale_ratio: 1.5 [sam] avg_coverage= 43.8x ERROR: gene= cyp2e1, profile= wxs, file= /home/ryan/NGS_Data/Exome_9-14-23/dragen_analysis/CYP-028/CYP-028.bam The average coverage of the sample is too low (1.9).

I have looked at the metrics for coverage for this particular sample and dragen reports 113X coverage over the target bed for the IDT exome capture probes. How should I resolve this? Thanks!

Edit: adding the debug info for one of these samples: debuginfo.tar.gz

[inumanag]

Hi @rrdavis77

I will soon release the version where you will be able to disable average coverage check (via --param min_avg_coverage=0).

(Duplicate: #49)