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Issue with unplaced contig naming in reference genome for array-analysis-cli (--gtc-to-vcf)

Status: Open.

#83 In Illumina/GTCtoVCF;

· leeyb9916 opened on Apr 30, 2025

Empty ALT genotypes?

Status: Open.

#81 In Illumina/GTCtoVCF;

· rajwanir opened on Apr 16, 2024

Tool assumptions and behaviour

Status: Open.

#80 In Illumina/GTCtoVCF;

· rajwanir opened on Apr 1, 2024

SB calculation

Status: Open.

#77 In Illumina/GTCtoVCF;

· marissa97 opened on Jul 12, 2023

Any experience about GQ settings

Status: Open.

#76 In Illumina/GTCtoVCF;

· AliceCheng7 opened on May 19, 2023

Python3 support

Status: Open.

#71 In Illumina/GTCtoVCF;

· Stikus opened on Nov 9, 2021

GQ score clarification

Status: Open.

#68 In Illumina/GTCtoVCF;

· Derrup opened on Nov 4, 2020

SourceSeq validation failures should be skipped instead of erroring out

bug

Status: Open.

#66 In Illumina/GTCtoVCF;

· jjzieve opened on Jul 28, 2020

Reference not detected if lowercase characters

question

Status: Open.

#64 In Illumina/GTCtoVCF;

· ghost opened on Jun 9, 2020

Unclear Error message

bug

Status: Open.

#59 In Illumina/GTCtoVCF;

· brianyiktaktsui opened on Dec 11, 2019

Replace ID in output VCF with <code>--id</code> option

enhancement

Status: Open.

#50 In Illumina/GTCtoVCF;

· stephenturner opened on Aug 28, 2019

Illumina Generated Manifest has no RefStrand column

question

Status: Open.

#49 In Illumina/GTCtoVCF;

· tbrunetti opened on Aug 7, 2019