Dear GATK team,
We are running GATK 3.5 with haplotypecaller and UnifiedGenotyper to consistent with our previous samples:
Command:
GenomeAnalysisTK.jar -T HaplotypeCaller -R $ref -S LENIENT -I input.bam --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -stand_call_conf 30.0 -stand_emit_conf 10.0 -ip 100 -rf BadCigar -o output.hap.g.vcf --dbsnp ${dbSNP} -nct 10
and: GenomeAnalysisTK.jar -T UnifiedGenotyper -R $ref -I input.bam -o output.unif.vcf -metrics UniGenMetrics -stand_call_conf 50.0 -stand_emit_conf 10.0 -dcov 1000 -A Coverage -A AlleleBalance -rf BadCigar -glm BOTH --dbsnp ${dbSNP} -nct10
However, the output of HaplotypeCaller don't have AF, AC. The MLEAF suppose to be equal to AF in this case?
e.g
output of Hap:
1 108310 rs74747225 T C, 391.77 . BaseQRankSum=2.485;ClippingRankSum=-0.083;DB;DP=48;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.364;RAW_MQ=111355.00;ReadPosRankSum=-0.440 GT:AD:DP:GQ:PGT:PID:PL:SB 0/1:34,13,0:47:99:0|1:108277_T_A:420,0,1881,522,1920,2442:21,13,6,7
output of Unit:
1 108310 rs74747225 T C 220.77 . ABHet=0.641;AC=1;AF=0.500;AN=2;BaseQRankSum=2.664;DB;DP=64;Dels=0.00;ExcessHet=3.0103;FS=1.104;HaplotypeScore=1.9874;MLEAC=1;MLEAF=0.500;MQ=41.95;MQ0=9;MQRankSum=-4.709;QD=3.45;ReadPosRankSum=-0.870;SOR=0.534 GT:AD:DP:GQ:PL 0/1:41,23:64:99:249,0,851
Thanks a lot.