Add an argument to set the separator in the replace_gt_with_sample.sh script and change default

scholl-lab / vcf-filtering

A collection of scripts for filtering annotated variant call format files

MIT License

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Add an argument to set the separator in the replace_gt_with_sample.sh script and change default #5

Closed berntpopp closed 9 months ago

berntpopp commented 10 months ago

When we convert the tsv values using replace_gt_with_sample.sh and the GT field has only numbers and they are separated by comma, excel converts these to numbers.

Solution:

add an argument to set the separator
change default to ";"