remove field from tab seperated file using awk -
i trying clean-up tab-delineated files , thought awk
below remove field 18 otherinfo
file. tried cut
, can not seem desired output. thank :).
file
chr start end ref alt func.refgene gene.refgene genedetail.refgene exonicfunc.refgene aachange.refgene popfreqmax clinsig clndbn clnacc clndsdb clndsdbid common otherinfo chr1 949654 949654 g exonic isg15 . synonymous snv isg15:nm_005101:exon2:c.294a>g:p.v98v 0.96 . . . . . . 1 3825.28 624 chr1 949654 . g 3825.28 pass af=1;ao=621;dp=624;fao=399;fdp=399;fr=.;fro=0;fsaf=225;fsar=174;fsrf=0;fsrr=0;fwdb=0.00425236;fxx=0.00249994;hrun=1;len=1;mlld=97.922;oalt=g;oid=.;omapalt=g;opos=949654;oref=a;pb=0.5;pbp=1;qd=38.3487;rbi=0.0367904;refb=0.0353003;revb=-0.0365438;ro=2;saf=335;sar=286;srf=0;srr=2;ssen=0;ssep=0;sssb=0.00332809;stb=0.5;stbp=1;type=snp;varb=-3.42335e-05;ann=isg15 gt:gq:dp:fdp:ro:fro:ao:fao:af:sar:saf:srf:srr:fsar:fsaf:fsrf:fsrr 1/1:171:624:399:2:0:621:399:1:286:335:0:2:174:225:0:0 399 reads
desired output
chr start end ref alt func.refgene gene.refgene genedetail.refgene exonicfunc.refgene aachange.refgene popfreqmax clinsig clndbn clnacc clndsdb clndsdbid common chr1 949654 949654 g exonic isg15 0 synonymous snv isg15:nm_005101:exon2:c.294a>g:p.v98v 0.96 . . . . . .
awk (runs doesn't remove field 18)
awk '{ $18=""; print }' file1
cut (removes field except 18)
cut -f18 file1
by default, awk uses blanks delimiters. therefore, have specify use tabs delimiters in output (ofs
):
awk 'begin{fs=ofs="\t"}{$18=""; gsub(/\t\t/,"\t")}1' file1
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