Hi,
When I run HaplotypeCaller on my files, the following four calls that are present in g.vcf but not in the vcf file.
1 116268178 . GAAAAA G,GA,GAA,GAAA,GAAAA,GAAAAAA, 329.70 . BaseQRankSum=1.030;ClippingRankSum=0.000;DP=123;ExcessHet=3.0103;MLEAC=0,0,0,1,0,0,0;MLEAF=0.00,0.00,0.00,0.500,0.00,0.00,0.00;MQRankSum=0.000;RAW_MQ=442800.00;ReadPosRankSum=-0.512 GT:AD:DP:GQ:PL:SB 0/4:13,3,7,5,9,15,7,0:59:6:366,202,1644,30,1203,1110,34,800,704,720,0,407,289,352,397,41,151,6,53,77,237,361,517,306,263,157,135,726,376,950,780,729,528,337,622,1005:3,10,14,32
8 144990528 rs7014582 A G, 3.42 . BaseQRankSum=0.431;ClippingRankSum=0.000;DB;DP=4;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=14400.00;ReadPosRankSum=0.000 GT:AD:DP:GQ:PL:SB 0/1:1,2,0:3:1:26,0,1,29,7,36:0,1,0,2
10 21461410 . GAA G,GA,GAAAA,GAAA, 0.01 . BaseQRankSum=-0.668;ClippingRankSum=0.000;DP=238;ExcessHet=3.0103;MLEAC=0,1,0,0,0;MLEAF=0.00,0.500,0.00,0.00,0.00;MQRankSum=0.000;RAW_MQ=856800.00;ReadPosRankSum=-1.739 GT:AD:DP:GQ:PL:SB 0/2:154,9,22,2,8,0:195:9:9,285,5620,0,3883,3558,638,6170,4167,12729,374,3649,3047,4219,3611,566,5114,3938,5749,3945,5146:71,83,17,24
20 42788826 . C A, 6.79 . BaseQRankSum=-0.524;ClippingRankSum=0.000;DP=6;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=21600.00;ReadPosRankSum=0.000 GT:AD:DP:GQ:PL:SB 0/1:3,2,0:5:34:34,0,72,43,78,122:2,1,1,1
There are about 433775 calls in the gvcf file and except the above four, the rest calls are present in the VCF file. I dont see any specific pattern why only these 4 are not present in the VCF.
The code I ran to produce the g.vcf and vcf files are:
gatk -T HaplotypeCaller --input_file cleaned.bam --out cleaned.g.vcf --reference_sequence Homo_sapiens_assembly19.fasta --intervals ROI_hg19.interval_list --dbsnp dbsnp_138.b37.vcf -stand_call_conf 30 -mbq 10 --min_mapping_quality_score 17 -ERC BP_RESOLUTION
gatk -T GenotypeGVCFs --variant cleaned.g.vcf --reference_sequence sapiens_assembly19.fasta --dbsnp dbsnp_138.b37.vcf --out cleaned.allbase.vcf --intervals hg19.interval_list -stand_call_conf 30 -allSites