Question: Copy Sample ID from VCF file to ID column
0
gravatar for waqasnayab
3.4 years ago by
waqasnayab200
Pakistan
waqasnayab200 wrote:

Hi,

I have a VCF file. If any of the sample has genotype 0/1 and 1/1, than the sample ID of such genotype should be pasted into the ID column like (I am just putting here ID and sample column):

ID sample1 sample2 sample3
rs123456 0/0 0/1 0/1 
rs789101 1/1 0/0 0/1
rs11213145 0/0 1/1 0/0

My desired output would be:

ID sample1 sample2 sample3
rs123456:sample2:sample3 0/0 0/1 0/1 
rs789101:sample1:sample3 1/1 0/0 0/1
rs11213145:sample2 0/0 1/1 0/0

Any awk or sed would be helpful, searches available to copy the contents of the column to the desired column but not for header (as header here is sample1 etc)

Thanks,

Waqas.

sequencing snp next-gen genome • 1.2k views
ADD COMMENTlink modified 3.4 years ago by Pierre Lindenbaum134k • written 3.4 years ago by waqasnayab200
3
gravatar for Pierre Lindenbaum
3.4 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum134k wrote:

assuming your VCF is really a VCF file and using bioalcidae http://lindenb.github.io/jvarkit/BioAlcidaeJdk.html

 java -jar dist/bioalcidaejdk.jar  -e 'println("ID\t"+header.getSampleNamesInOrder().stream().collect(Collectors.joining("\t")));stream().filter(V->V.hasID()).forEach(V->println(V.getID()+":"+V.getGenotypes().stream().filter(G->G.isHet()||G.isHomVar()).map(G->G.getSampleName()).collect(Collectors.joining(":"))+"\t"+header.getSampleNamesInOrder().stream().map(S->V.getGenotype(S).getAlleles().stream().map(A->String.valueOf(V.getAlleleIndex(A))).collect(Collectors.joining("/"))).collect(Collectors.joining("\t"))));' input.vcf
ADD COMMENTlink written 3.4 years ago by Pierre Lindenbaum134k

YES, Pierre, it worked for me, although just cross-checking a bit, will further confirm this command...,,,!!!!!

ADD REPLYlink written 3.4 years ago by waqasnayab200
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