Hey, we are using GATK4 plus denovogear/1.1.1 to calculate the denovo variants at whole genome level for a small cohort, but we are running into the issues of interpreting the output of denovogear.
here is one of the problematic sites form our original vcf file,the first sample is the offspring, and we used the dng dnm to call the denovo variants
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 290_S1 291_S1 292_S1
first, it looks more like an indel instead of snp to us, second, we have no idea where the genotype T from. could you please take a look to see if that is a sound denovo prediction? I am also wondering if denovogear are able to deal with the spanning or overlapping deletions, like the sites with *? Thanks!
Hey, we are using GATK4 plus denovogear/1.1.1 to calculate the denovo variants at whole genome level for a small cohort, but we are running into the issues of interpreting the output of denovogear.
here is one of the problematic sites form our original vcf file,the first sample is the offspring, and we used the dng dnm to call the denovo variants
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 290_S1 291_S1 292_S1
chr16 6548257 . C A,* 10656.38 PASS AC=0,1;AF=0.00,0.167;AN=6;BaseQRankSum=2.63;ClippingRankSum=0.00;DP=96;ExcessHet=8.0462;FS= 0.517;InbreedingCoeff=-0.1581;MQ=49.47;MQRankSum=0.00;QD=14.95;ReadPosRankSum=-7.790e-01;SOR=0.633;VQSLOD=9.18;culprit=DP GT:AD:DP:GQ:PGT:PID:PL 0/2 :18,0,16:34:99:0|1:6548256_AC_A:388,445,1193,0,748,700 0/0:20,3,0:23:38:.:.:0,38,685,60,692,715 0/0:39,0,0:39:81:.:.:0,81,1062,81,1062,1062
the output is like this: DENOVO-SNP CHILD_ID: 290_S1 chr: chr16 pos: 6548257 ref: C alt: A,* maxlike_null: 4.83092e-09 pp_null: 0.796708 tgt_null(child/mom/dad): CT/AT/CC snpcode: 3 code: 9 maxlike_dnm: 9.9301e-09 pp_dnm: 0.203292 tgt_dnm(child/mom/dad): CT/CC/CC lookup: 4 flag: 1 READ_DEPTH child: 34 dad: 39 mom: 23 MAPPING_QUALITY child: -2147483648 dad: -2147483648 mom: -2147483648
first, it looks more like an indel instead of snp to us, second, we have no idea where the genotype T from. could you please take a look to see if that is a sound denovo prediction? I am also wondering if denovogear are able to deal with the spanning or overlapping deletions, like the sites with *? Thanks!