crazyhottommy · August 24, 2015 16:38
diff --git a/sub_shell_maintain_header.sh b/sub_shell_maintain_header.sh
 # output of mutect run for each chromosome
 # the first line is the mutect version, the second line is the header
 # keep the header and filter mutect results based on 10th and 35th columns.

 for file in *.call.txt
 do (sed -n '2p' $file; awk -F "\t" '$10=="COVERED" && $35=="KEEP"' $file) > ./keep/"${file%txt}"keep.txt
 done
	# output of mutect run for each chromosome
	# the first line is the mutect version, the second line is the header
	# keep the header and filter mutect results based on 10th and 35th columns.

	for file in *.call.txt
	do (sed -n '2p' $file; awk -F "\t" '$10=="COVERED" && $35=="KEEP"' $file) > ./keep/"${file%txt}"keep.txt
	done
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