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Kurt-Hetrick / JHG_Clincal_Exome_Pipeline

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bug in *.VQSR.PASS.SNV.KinshipIBS.txt output in pca/relatedness script #25

Closed Kurt-Hetrick closed 3 years ago

Kurt-Hetrick commented 3 years ago

when trying to reimplement this I am getting a syntax error.

awk: cmd. line:1: NR>1 $15>0.06 {print $1,$2,$3,$4,"0",$5,$6,$7,$8,$9,$10,$11,$12,$13,$14,$15,"1"} \
awk: cmd. line:1:         ^ syntax error

when looking at a log i don't see the syntax error (maybe only stdout is captured and not stderr?), but in any case an output file is created...however, it doesn't look like the original intent of the output is done correctly. a record in kin0 is duplicated with both a 0 and 1 added to a last field, but it looks like it was supposed to be one or the other depending on the value in field 15.

Kurt-Hetrick commented 3 years ago

bug fixed in phase2 branch