Question: Copy Sample ID from VCF file to ID column
0
gravatar for waqasnayab
23 months ago by
waqasnayab180
Pakistan
waqasnayab180 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 • 820 views
ADD COMMENTlink modified 23 months ago by Pierre Lindenbaum122k • written 23 months ago by waqasnayab180
3
gravatar for Pierre Lindenbaum
23 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum122k 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 23 months ago by Pierre Lindenbaum122k

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

ADD REPLYlink written 23 months ago by waqasnayab180
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