Title: Enhance replace_gt_with_sample.sh to Handle Non-1 GT Fields
Description:
Update the replace_gt_with_sample.sh script to properly handle genotypes (GT fields) that are not equal to 1. This enhancement should include logic to correctly interpret and process various GT field values, ensuring accurate genotype replacement.
Acceptance Criteria:
Modify replace_gt_with_sample.sh to detect and handle GT fields with values other than 1.
Ensure the script can correctly interpret phased (|) and unphased (/) genotypes.
Add error handling and logging for unsupported or unexpected GT field values.
Update the script's documentation to reflect the new capabilities and usage instructions.
Impact: This will improve the accuracy of genotype replacements and expand the script's compatibility with different VCF file formats.
Title: Enhance
replace_gt_with_sample.shto Handle Non-1 GT FieldsDescription: Update the
replace_gt_with_sample.shscript to properly handle genotypes (GT fields) that are not equal to 1. This enhancement should include logic to correctly interpret and process various GT field values, ensuring accurate genotype replacement.Acceptance Criteria:
replace_gt_with_sample.shto detect and handle GT fields with values other than 1.Impact: This will improve the accuracy of genotype replacements and expand the script's compatibility with different VCF file formats.