Trying to understand BWA output and what it could mean? Please help!

Question

[screadore]

Hello everyone,

So I used BWA to align Read 1 and Read 2 of my whole genome sequence (WGS) and I'm trying to interpret the results accurately.

Total PF = 100%

Paired = 99.87%

Read 1 = 49.93%

Read 2 = 49.93%

Aligned = 41.41%

Properly paired = 95.69%

Singletons = 1.47%

Secondary Alignments = 0.32%

Duplicates = 12.63%

Does this mean that since they are so aligned they could show heterozygosity and then a disease causing gene would be recessive? or what is your take on it? Please help.

Answer 1

[JC]

Does this mean that since they are so aligned they could show heterozygosity and then a disease causing gene would be recessive?

No, it just says that your reads were mapped almost all of them (95.69% as properly paired) and a few ones has issues: singletons = only one pair mapped correctly, secondary alignments = some reads have a second good match, duplicates = some reads seems to be duplicated (same sequence and quality scores)

To answer your question you need to check where are they aligned, coverages, SNPs, etc.

[screadore]

Thank you so much! How could I check that?

[JC]

You are just at the beginning, after alignment, you need to call variants and then you can check for disease-causing variants, check the process in GATK https://gatk.broadinstitute.org/hc/en-us/categories/360002302312, and prioritize variants with VEP, Gemini, Exomiser, etc.