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# 1. Test ExAC allele frequencies

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check()

{

if diff $1 $2; then

echo ok

else

echo fail

fi

}

export -f check

echo " exac.t01...\c"

echo "chrom start end ref alt in_exac aaf_exac_all aaf_adj_exac_all aaf_adj_exac_afr aaf_adj_exac_amr aaf_adj_exac_eas aaf_adj_exac_fin aaf_adj_exac_nfe aaf_adj_exac_oth aaf_adj_exac_sas

chr1 985954 985955 G C 0 None None None None None None None None None

chr1 1199488 1199489 G A 0 None None None None None None None None None

chr1 1959698 1959699 G A 1 0.017 0.0175763511709 0.00489987217725 0.00975699558174 0 0.0412407472682 0.0237794612795 0.0224438902743 0.00647021140295

chr1 161276552 161276553 G T 0 None None None None None None None None None

chr1 247587092 247587093 C T 0 None None None None None None None None None

chr9 112185055 112185056 C G 1 8.236e-06 8.23709658819e-06 0 0 0 0 1.49853143919e-05 0 0

chr12 121432116 121432118 GC G 1 0.243 0.278784178031 0.215484048405 0.486200895077 0.00100267379679 0.317728531856 0.330323021843 0.255813953488 0.109512269009

chr14 105420589 105420590 C T 1 0.001735 0.00174129353234 0.00030637254902 0.000777873811582 0 0.00030238887209 0.00246261036699 0.00447427293065 0.00169594185342" > exp

gemini query --header -q "select chrom, start, end, ref, alt, in_exac, aaf_exac_all, aaf_adj_exac_all, \

aaf_adj_exac_afr, aaf_adj_exac_amr, aaf_adj_exac_eas, aaf_adj_exac_fin, \

aaf_adj_exac_nfe, aaf_adj_exac_oth, aaf_adj_exac_sas from variants" test.exac.db > obs

check obs exp

rm obs exp

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