understanding snpEff/snpSift concordance output

Question

[rcappa]

Hello,

I have numerous samples which were sequenced, and then genotyped, resulting in two VCF with the same samples in each. I am hoping to calculate the percentage concordance between the files on a sample by sample basis. I have used the snpEff/snpsift concordance command, but I do not understand the column headings of the output file. Any help in understanding the meaning of these headings and/or advice on which columns to use when calculating concordance would be greatly appreciated.

The output column headings are as follows;

output column headings;

MISSING_ENTRY_array/MISSING_ENTRY_WGS

MISSING_ENTRY_array/MISSING_GT_WGS

MISSING_ENTRY_array/REF

MISSING_ENTRY_array/ALT_1

MISSING_ENTRY_array/ALT_2

MISSING_GT_array/MISSING_ENTRY_WGS

MISSING_GT_array/MISSING_GT_WGS

MISSING_GT_array/REF

MISSING_GT_array/ALT_1

MISSING_GT_array/ALT_2

REF/MISSING_ENTRY_WGS

REF/MISSING_GT_WGS

REF/REF

REF/ALT_1

REF/ALT_2

ALT_1/MISSING_ENTRY_WGS

ALT_1/MISSING_GT_WGS

ALT_1/REF

ALT_1/ALT_1

ALT_1/ALT_2

ALT_2/MISSING_ENTRY_WGS

ALT_2/MISSING_GT_WGS

ALT_2/REF

ALT_2/ALT_1

ALT_2/ALT_2

ERROR

[anamaria]

Hi,

can you please tell me if you figured out what those represent and how to interpret the result?

Answer 1

[sara.wennersten]

Hi, Have you figured out how to interpret the results? Thanks!