The previous steps each mention inputs making but Step 5 is missing mention of gatk4_pon_genomicsdbimport_make_input.sh
When I use it, it creates a faulty sample map file because line 66 is
The delimiter required by GATK is Tab but it is actually a series of spaces in the file. This leads to all intervals failing:
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A USER ERROR has occurred: Bad input: Expected a file with 2 fields per line in the format
Sample File
but found line: "OSCC_1-N ./all4SetsNormal_PoN/OSCC_1-N.pon.vcf.gz" with 1 fields
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Because the -e setting is already used, the script ought to use \t to represent a tab.
DESCRIPTION
Echo the STRING(s) to standard output.
-n do not output the trailing newline
-e enable interpretation of backslash escapes
tracychew
commented
2 years ago
The previous steps each mention inputs making but Step 5 is missing mention of
gatk4_pon_genomicsdbimport_make_input.shWhen I use it, it creates a faulty sample map file because line 66 isThe delimiter required by GATK is Tab but it is actually a series of spaces in the file. This leads to all intervals failing:
Because the
-esetting is already used, the script ought to use\tto represent a tab.