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Why is NA18498 sample missing from 1000 genome GRCh38 vcf file?

Hi I am trying to compare the 1000 genome phase3 GRCh19 vcf file and the GRCh38 （low coverage） vcf file.

I noticed that one sample, NA18498, is present in the GRCh19 file but not in the GRCh38 file. I could not find a document and any other source that confirms this information. Does anyone know why this sample is missing from the GRCh38 vcf file and where I can find more details about it?

I have also noticed that there are 45 more samples in the GRCh38 version file, such as HG00270, HG03398, HG03393. I am not sure why they were introduced

Thank you for your help.

Regrads

Zhang

Resource:

GRCh19 1000 genomes: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/

GRch38 1000 genomes (low coverage): http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/

ngs vcf 1000 1kg genome
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written by octpus616 • octpus616

1 answer

If I am not mistaken, the GRCh38 files you relate to only contain unrelated samples, that's why NA18498 is not included.

• 0 views • link
written by DBScan • DBScan

yeah, but GRCh19 seems also only contain unrelated sample, the NA18498 also including in GRCh19 and GRCh38 1000 genomes (high coverage) unrelated panel

• 0 views • link
written by octpus616 • octpus616

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