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How can I compare two columns of a two VCF files

How can I compare two columns of a VCF file (i.e. chromosome number and position) and return the entire row if both the position and chromosome number match in two diffrent VCF files? The following awk command works to compare one column what changes can I make in it to make it compare two columns together.

awk 'FNR==NR{a[$1]=$0;next}{if(b=a[$1]){print b}}' fileA fileB > out
next-gen snp
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updated by Ram Ram • written by kinsioberoi • kinsioberoi

Can you please post an example of the input and desired output? Thanks.

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updated by Ram Ram • written by bioguy24 bioguy24

so for example if File A and B are as following the code with match the 1st column (#CHROM) and the 2nd column(POS) and return the output from A which is matching

File A

#CHROM  POS     ID            REF  ALT
chr1    64      rs3883910     C    T
chr2    146     .             G    A
chr2    146     rs72619361    T    C

File B

#CHROM    POS     ID           REF  ALT
chr1      64      rs3883910    C    T
chr1      146     rs982818     C    T
chr2      146     rs72619361   T    C

OUTPUT

#CHROM    POS      ID            REF  ALT
chr1      64       rs3883910     C    T
chr2      146      rs72619361    T    C
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updated by Ram Ram • written by kinsioberoi • kinsioberoi

return the entire row if both the position and chromosome number match in two diffrent VCF files.

Return from which file? FileA or FileB?

May be this vcftools solution will work for you.

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updated by Ram Ram • written by venu venu

2 answers

Looks like you want to intersect two VCF files. There's already software to do it and its much cleaner to use them than write a messy one-liner. Check Bedtools intersectBed.

http://bedtools.readthedocs.org/en/latest/content/tools/intersect.html

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written by Vivek Vivek

You can also use VCFtools (available here) to compare VCFs.

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updated by Ram Ram • written by harold.smith.tarheel harold.smith.tarheel

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