Variant missing in WGS sample

Question

[adarsh_pp]

Hi,

I have processed a WGS sample including alignment (bwa-mem2), variant calling (GATK HaplotypeCaller) and annotation (ANNOVAR). In the annotated file, a variant fitting the phenotype was identified. However, on visualizing the bam in IGV, this variant was not there.

What could be the possible reasons for this?

Will the newly aligned intermediate bam file generated by HaplotypeCaller contains this variant?

Please let me know.

Thank you

Answer 1

[Raony Guimarães]

Depends on what you did while processing your bam file.

What was the the DP,PL,GQ, and read counts for each allele of the variant?

Did you remove duplicates, run base quality score recalibration and local realignment around indels in your bam file? All these can remove good and bad variants from your bam file.