Regions not clear in VCF

Question

[priya.bmg]

Hello,

Has anyone come across the below results in vcf with both alleles as wild type and variant. I am not sure where to start checking. Any thoughts

Chr Start            End          Ref   Alt 
chr9    127447499   127447499   A   -   
chr9    127447499   127447499   -   A

Does it mean that there is sometimes a deletion (first line) and there is also insertion of A (second line). Still unclear as individuals carry same genotype in same position. For example, individual A has 0/3, 0/3 genotypes in both positions

Thank you

[Pierre Lindenbaum]

Regions not clear in VCF

FYI, this is not a VCF.

[Pierre Lindenbaum]

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• Sequencing old DNA samples
• PacBio Raw Data File Formats
• Pacbio workflow
• Hard filtering variants
• Filtering of rare variants
• Shared variants
• Exec format error in unmapped bam file
• Snakemake bwa mem
• Read group info
• Alignment using bwa-mem2
• Reference file for base recalibration
• Bowtie2 aligner
• Random Boolean network with same input nodes as original network
• Genes inhibiting each other's expression