bcftools ignores indel even when using --min-ireads 10
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Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 30/100
- Issue type
- Bug
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- c
- Domain
- bioinformatics
Research direction
Start by reproducing the supplied bcftools mpileup and call command with and without --ignore-overlaps and --min-ireads 10. Compare the resulting VCF fields for the deletion, especially IDV, DP, and AD, and trace how the reported indel is handled. Done means the behavior is explained and the issue is resolved or the expected behavior is documented.
Written by the indexing model from the issue text.
Description
I tried variant calling using bcftools using recommended settings for SARS-Cov-2 i.e. using --ignore-overlaps --min-ireads 10 on my ISeq Illumina data. However, I can see that a deletion supported by 30 reads is being ignored (I reran without above flags and compared the vcf files). For some reason IDV=9. Below attached the coverage of the deletion and the coverage plot
bcftools mpileup --redo-BAQ --max-depth 0 --min-BQ 20 --min-MQ 20 --count-orphans --fasta-ref ../00_index/Sars_cov_2.ASM985889v3.dna.toplevel.fa --annotate AD \
--ignore-overlaps --min-ireads 10 16_S16_L001.dedup.bam | bcftools call --multiallelic-caller --variants-only --ploidy 1 --output-type b - > temp2.bcftools.bcf
MN908947.3 28361 . GGAGAACGCAG GG 225 . INDEL;IDV=9;IMF=1;DP=9;VDB=0.156835;SGB=-0.662043;MQ0F=0;AC=1;AN=1;DP4=0,0,0,9;MQ=60 GT:PL:AD 1:255,0:0,9
- Dominant language
- C
- Stars
- 891
- Forks
- 277
- Avg merge
- 2d 23h
- Merged PRs (30d)
- 2
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