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Fastest Way To Rename Sample Name In 37 Gb Gzipped Vcf File Or Binary Ped File

Hi I have a project file for 2000 individuals, with SNPs from WGS. We have decided to change the sample names to a more uniform way of naming individuals from different sources.

I wish to do a quick check if there's inbuilt functions in plink or plink seq or vcftools to do this i.e. pass it a sample name remapping file to output a new set of fam ids and idv ids.

Otherwise, i might consider doing this using sqlite since there's a possibility I might have to slice the data in another way again

vcf ped bed
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updated by Ram Ram • written by Kevin Kevin

Hi, running into an identical problem here. Do you recall how you ended up doing this?

Thanks in advance,
Steve

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updated by Ram Ram • written by stevenlang123 stevenlang123

2 answers

As long as you do NOT (i) change the order or (ii) remove/add individuals you can edit the FAM file for ids. My recommendation would be a script to do the correction on the FAM file.

Remember: the order and the number of individuals stay the same. Other than that, you can change the FAM ids

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written by tiagoantao tiagoantao

You could create a new vcf header with the final #CHROM line updated to reflect the new sample names. Then use tabix to replace the older header with the new one.

# Replace VCF header. The file must be compressed by bgzip. 
tabix -r header.txt big.vcf.bgz > big.vcf.new_header.bgz

More here: http://vcftools.sourceforge.net/docs.html#one-liners

Edit: To get your VCF in the correct format and to create the tbi index do something like...

gunzip -c big.vcf.gz | bgzip > big.vcf.bgz
tabix -p vcf big.vcf.bgz
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written by Nick Crawford Nick Crawford

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