Sample Type: genome_as_fake_exome, exome or custom_capture
Sample Phenotype: case or ctrl
GT: hom re, het or hom
DP: variant caller DP
DP Bin: calculated from BAM, values: NA (0-9), 10 (10-19), 20 (20-29), 30 (30-49), 50 (50-199), 200 (200+)
AD REF: quality stat from GATK
AD ALT: quality stat from GATK
Percent Alt Read: percentage of all the reads at the site that support the alternative allele
Percent Alt Read Binomial P: binomial Exact one-tail p-value permitted for the alt:ref ratio discrepancy from expected 0.5
GQ: quality stat from GATK
VQSLOD
SOR: quality stat from GATK
FS: quality stat from GATK
MQ: quality stat from GATK
QD: quality stat from GATK
Qual: quality stat from GATK
Read Pos Rank Sum: quality stat from GATK
MQ Rank Sum: quality stat from GATK
FILTER: Filter is based on GATK's VQSR method. We defined four tranches: PASS, LIKELY, INTERMEDIATE, FAIL. Pass has the lowest sensitivity for detecting true variants, but is very specific. Each subsequent tranche introduces additional true positive calls along with a growing number of false positive calls.