The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.

GenotypeVCFs provide wrong AC value ?

I did HaplotypeCaller + genotypeVCFs on 4 sample bam files (with low coverage/depth).
I saw that AC INFO field do not represent the sum of all alternate allele seen.

grep -we rs10753352 -we rs80146807 -we rs707592 trisomie.vcf
chr1    5184689 rs10753352      G       C       147.81  .       AC=4;AF=0.667;AN=6;DB;DP=7;FS=0.000;GQ_MEAN=6.00;GQ_STDDEV=6.00;MLEAC=5;MLEAF=0.833;MQ=93.02;MQ0=0;NCC=1;QD=24.64     GT:AD:DP:GQ:PL  1/1:0,4:4:12:116,12,0   ./.:0,0:0       1/1:0,2:2:6:59,6,0      0/0:1,0:1:0:0,0,8
chr1    5730409 rs80146807      G       T       142.09  .       AC=5;AF=0.625;AN=8;BaseQRankSum=0.804;ClippingRankSum=0.804;DB;DP=6;FS=0.000;GQ_MEAN=12.75;GQ_STDDEV=17.56;MLEAC=5;MLEAF=0.625;MQ=82.96;MQ0=0;MQRankSum=0.804;NCC=0;QD=26.86;ReadPosRankSum=0.804     GT:AD:DP:GQ:PL  0/0:1,0:1:3:0,3,45      1/1:0,1:1:3:45,3,0      1/1:0,2:2:6:90,6,0   0/1:1,1:2:39:39,0,62
chr1    5732382 rs707592        T       C       194.63  .       AC=5;AF=0.833;AN=6;BaseQRankSum=-7.360e-01;ClippingRankSum=0.736;DB;DP=9;FS=8.451;GQ_MEAN=13.33;GQ_STDDEV=8.08;MLEAC=5;MLEAF=0.833;MQ=26.49;MQ0=0;MQRankSum=0.736;NCC=1;QD=32.44;ReadPosRankSum=0.736 GT:AD:DP:GQ:PL  ./.:0,0:0       1/1:0,4:4:12:149,12,0   0/1:2,1:3:22:22,0,49    1/1:0,2:2:6:53,6,0

I join the corresponding ##GATKCommandLine in case.

If I misunderstand what AC is, feel free to teach me.


Best Answer


Sign In or Register to comment.