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Full Discussion: Compare fields in 2 files using AWK
Top Forums Shell Programming and Scripting Compare fields in 2 files using AWK Post 302464453 by bartus11 on Wednesday 20th of October 2010 08:06:18 AM
Old 10-20-2010
Code:
awk -F\| 'NR==FNR{a[NR]=$0;next}FNR==1{print;next}{split(a[FNR],b,"|");for (i=1;i<=NF;i++){if (i==1){printf $1};if (FNR!=1 && i!=1 && b[i]==$i){printf FS "y"};if (FNR!=1 && i!=1 && b[i]!=$i){printf FS "n"};};printf "\n"}' file 1 file2

 

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LEARN ABOUT DEBIAN

vcf-compare

VCF-COMPARE(1)							   User Commands						    VCF-COMPARE(1)

NAME

       vcf-compare - compare bgzipped and tabix indexed VCF files

SYNOPSIS

       compare-vcf [OPTIONS] file1.vcf file2.vcf ...

DESCRIPTION

       About: Compare bgzipped and tabix indexed VCF files. (E.g. bgzip file.vcf; tabix -p vcf file.vcf.gz)

OPTIONS

       -c, --chromosomes <list|file>
	      Same as -r, left for backward compatibility. Please do not use as it will be dropped in the future.

       -d, --debug
	      Debugging information. Giving the option multiple times increases verbosity

       -H, --cmp-haplotypes
	      Compare haplotypes, not only positions

       -m, --name-mapping <list|file>
	      Use  with -H when comparing files with differing column names. The argument to this options is a comma-separated list or one mapping
	      per line in a file. The names are colon separated and must appear in the same order as the files on the command line.

       -R, --refseq <file>
	      Compare the actual sequence, not just positions. Use with -w to compare indels.

       -r, --regions <list|file>
	      Process the given regions (comma-separated list or one region per line in a file).

       -s, --samples <list>
	      Process only the listed samples. Excluding unwanted samples may increase performance considerably.

       -w, --win <int>
	      In repetitive sequences, the same indel can be called at different positions. Consider records this far apart as matching (be  it  a
	      SNP or an indel).

       -h, -?, --help
	      This help message.

vcf-compare 0.1.5						     July 2011							    VCF-COMPARE(1)
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