ceph/ utah pedigree 1463 members no difference in genomic data
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7.3 years ago
gulcek ▴ 20

Among (maternal) grandmother and grandfather of utah pedigree 1463, I cannot find any difference in their genomic data. I use snp rsids, alleles, chromosome ad its beginning point to compare different members genomic data. I compare their snp alleles, but only different alleles are in the chromosome X and Y snps. I also tried the same thing in 1000 genome project YRI trio data and could not find any difference among them. In both cases the members I compare have not any kinship. I downloaded all files from 1000 genome project and I use dbSNPAnnotated assembly files. Although their genomic information should be different as much as strangers, why do I obtain the same genomes?

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Something is obviously wrong. Can you post the programs and parameters you are using?

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The columns in dbSNPannotated file is in this way:

dbSnpId    alleles    chromosome    begin    end    reference    alleleAGenotype    alleleBGenotype    loci    so on..
dbsnp.132:rs112750067    C/T    chr1    10326    10327    T    NO-CALL    NO-CALL    2    no-call    no-call

I extract the first 5 columns of the file and then compare them by diff:

diff -u mother.txt father.txt > difference.txt

I also tried this in other trios but the result is same, not difference except sex chromosomes. What do I do wrong?

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