Created
March 21, 2016 21:21
-
-
Save gatoravi/35a216099a88081a3329 to your computer and use it in GitHub Desktop.
Convert hcc1395 tsv to vcf
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| awk '{ gsub("\,", "");gsub("\"", ""); gsub ("\r", "\n"); print }' SupplementaryData1_Tier1_SNVs.txt | awk 'BEGIN { print "##fileformat=VCFv4.1\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO" } !/Chrom/ { if($1 !~ /GL/) print $1"\t"$2"\t.\t"$4"\t"$5"\t.\tPASS\t." }' > hcc1395_somatic.vcf |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment