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xihaoli / STAARpipeline-Tutorial

The tutorial for performing single-/multi-trait association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using FAVORannotator, STAARpipeline and STAARpipelineSummary
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Can't annotate individual variant results #56

Closed GACGAMA closed 2 months ago

GACGAMA commented 2 months ago

Hello Xihao! The results from individual analysis are outputted as such:

CHR POS REF ALT etc...

I'm trying to annotate these results using common tools to explore (such as VEP) But the problem is: Deletions are annotated as:

CHR POS REF ALT
1   943528  T   *

And insertions:

CHR POS REF ALT
1   977780  AAT ACCAT

The problem: I can't seem to find a version o vcf in which insertions are annotated with the full insertion and deletions are annotated with * on ALT. Only versions of vcf which annotates insertions as . in the REF and deletions with . in the ALT

VEP can't keep with this way of annotating, which makes me lose my deletions when annotating.

Example of VEP output: WARNING: Line 815 skipped (1 77568473 A . 0.3299508 0.3299508 2767 0.0003...): Invalid allele string ./0.3299508 or possible parsing error

Do you have any suggestions? Could STAAR output a VCF formatted result as summary?

xihaoli commented 2 months ago

Hi @GACGAMA,

Thanks for reaching out. Sure, we plan to include this feature of STAAR in the to-do list hopefully soon. In the meantime, please feel free to prepare your data with your ideal input format in the VCF/aGDS file before running STAARpipeline. For individual variant analysis, such variant identification information (CHR-POS-REF-ALT) would not affect your analysis results.

Let me know if you have any questions.

Best, Xihao

GACGAMA commented 2 months ago

Thanks Xihao!