[Vcftools-help] Output of vcftools diff

[Laurent F. <lau...@gm...>]

Dear VCFTools Team,

I am trying to compare two VCF files containing the same individual (one
with sequence data, the other with immunochip data) using vcftools --diff
--diff-site-discordance --diff-discordance-matrix

I know that the documentation says that this functionality is likely buggy
and so this might be the root of my incomprehensions.

Here is the head of the .diff.sites:
CHROM    POS    FILES    MATCHING_ALLELES    N_COMMON_CALLED    N_DISCORD
DISCORDANCE
1    10009    2    0    0    0    nan
1    10109    2    0    0    0    nan
1    10150    2    0    0    0    nan
1    10180    2    0    0    0    nan
1    10234    2    0    0    0    nan
....

And here are the result of summing each of the columns:
Loci in file 1 only: 119529 (2.911%)
Loci in file 2 only: 978611 (23.832%)
Loci in both files: 3008166 (73.257%)
    Matching Alleles: 3006754 (99.953%)
    Common called: 3008166 (100.000%)
    Discordant: 64541 (2.146%)
    Discordance: 64541 (2.146%)

Here, I am not sure what the MATCHING_ALLELES, N_COMMON_CALLED and N_DISCORD
columns are exactly. Could you please explain those?


Now below is the output for the .diff.discordance_matrix:
                 N_0/0_file1     N_0/1_file1     N_1/1_file1     N_./._file1
N_0/0_file2     0       0       0       0
N_0/1_file2     2742    1879154 2914    0
N_1/1_file2     54656   2817    1064471 0
N_./._file2     0       0       0       0

Here I think everything is quite straight forward except that I do not have
any 0/0 loci any of the two files, yet there are non-0 values in the
N_0/0_file1 column. Could you please let me know how this could happen?

Thanks a lot,
Laurent



-- 
Laurent Francioli
PhD Student
UMC Utrecht