haplotypecaller output no AF

LZhLZh Member
edited March 2018 in Ask the GATK team

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,<NON_REF> 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.

Post edited by shlee on

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