Hom-ref Blocks FORMAT Fields
In hom-ref blocks, the following FORMAT fields are calculated uniquely.
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FORMAT/DP—Values represent the minimum DP across all positions within the band. |
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FORMAT/AD—Values represent the position in the band where DP=median DP. |
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FORMAT/AF—Values are based on FORMAT/AD. |
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FORMAT/PL—Values represent the Phred likelihoods per genotype hypothesis. For hom-ref blocks, each value in FORMAT/PL represents the minimum value across all positions within the band. |
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FORMAT/SPL and FORMAT/ICNT—Parameters reported in the gVCF records, including both hom-ref blocks and variant records. The parameters are used to compute the confidence score of a variant being de novo in the proband of a trio. For SNP, FORMAT/PL and FORMAT/SPL are both used as input to the DeNovo caller. FORMAT/PL represents Phred likelihoods obtained from the genotyper, if the genotyper is called. FORMAT/SPL represents Phred likelihoods obtained from column-wise estimation, pre-graph. Each value in FORMAT/SPL represents the minimum across all positions within the band. For INDEL, the PL value is computed in the joint pedigree calling step based on the FORMAT/ICNT reported in the gVCF file. FORMAT/ICNT consist of two values. The first value is the number of reads with no indels at the position, and the second value is the number of reads with indels at the position. Each value in FORMAT/ICNT represent the maximum of the value across all positions within the band. |
In the following example hom-ref block, ICNT provides information on if each sample contains an Indel at the position of interest. If the proband contains an indel at the position and the ICNT of the parents does not indicate any read supporting an indel, then the confidence score is high for the proband to have an indel de novo call at the position.
chr1 10288 . C <NON_REF> . PASS END=10290 GT:AD:DP:GQ:MIN_DP:PL:SPL:ICNT 0/0:131,4:135:69:132:0,69,1035:0,125,255:23,1
chr1 10291 . C
T,<NON_REF> 38.45 PASS DP=100;MQ=24.72;MQRankSum=0.733;ReadPosRankSum=4.112;FractionInformativeReads=0.600;R2_5P_bias=0.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:SPL:ICNT:GP:PRI:SB:MB 0/1:28,32,0:0.533,0.000:60:20,21,0:8,11,0:15:73,0,12,307,157,464:255,0,255:23,10:3.8452e+01,1.3151e-01,1.5275e+01,3.0757e+02,1.9173e+02,4.5000e+02:0.00,34.77,37.77,34.77,69.54,37.77:4,24,7,25:8,20,14,18
The SPL and ICNT is specific to DRAGEN. The GATK variant caller does not output the SPL and ICNT values.
