ExpansionHunter extract sex from a ped file. #281
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mwalker174
requested changes
Jan 10, 2022
wdl/ExpansionHunter.wdl
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| sex="" | ||
| if [ ! -z "~{ped_filename}" -a "~{ped_filename}" != " " ]; then | ||
| if [ -e "~{ped_filename}" ]; then | ||
| sex=$(awk -F '\t' '{if ($2 == "~{individual_id}") {if ($5 == "1") {print "--sex male"; exit 0} else if ($5 == "2") {print "--sex female"; exit 0} else {exit 1}}}' < ~{ped_filename} ) |
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I would actually try to emit a helpful error message if the sex is undefined. I think it would be best to define sex="NA" if the ped file is provided. Then use print "NA"; exit 0 instead of exit 1 in the last if clause. Then check the value of sex below - if it's NA then warn that either the sample id was not found or the sex is undefined and fail.
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Please check if the updated condition would be equally good.
Co-authored-by: Mark Walker <[email protected]>
Co-authored-by: Mark Walker <[email protected]>
Co-authored-by: Mark Walker <[email protected]>
Co-authored-by: Mark Walker <[email protected]>
Co-authored-by: Mark Walker <[email protected]>
mwalker174
approved these changes
Jan 11, 2022
Co-authored-by: Mark Walker <[email protected]>
Co-authored-by: Mark Walker <[email protected]>
# Conflicts: # wdl/ExpansionHunter.wdl
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EH processes male and female samples differently; this PR adds a functionality where sample sex is extracted from a provided
PEDfile.