samtools
concordance with indels issue
I am trying to compare two vcfs, specifically indels and the concordance is incorrect. It says the two vcfs for the first individual are AA Het -> AA Het but it should be AA Het to AA Hom. Any insight appreciated!
Truth region
##bcftools_viewVersion=1.21+htslib-1.21 ##bcftools_viewCommand=view -r NW_026622797.1:20902219-20902230 combined_genotype_output.vcf.gz; Date=Thu Mar 27 14:52:44 2025 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT BB_WSU_973 BB_WSU_974 BB_WSU_975 BB_WSU_Adak BB_WSU_Cooke BB_WSU_Dodge BB_WSU_Frank BB_WSU_John BB_WSU_Oakley BB_WSU_Willow BB_WSU_Zuri NW_026622797.1 20902219 . G GCACA,GCACACACA,GCACGCACA,GCACGCACACACA,GCACACA 7722.9 . AC=6,2,1,3,1;AF=0.273,0.091,0.045,0.136,0.045;AN=22;BaseQRankSum=-0.38;DP=417;ExcessHet=0.7463;FS=2.188;InbreedingCoeff=0.0598;MLEAC=6,2,1,3,1;MLEAF=0.273,0.091,0.045,0.136,0.045;MQ=59.93;MQRankSum=0;QD=27.98;ReadPosRankSum=0.781;SOR=0.843 GT:AD:DP:GQ:PL 2/5:0,0,8,0,0,12:20:99:870,734,682,336,330,274,734,682,330,682,734,682,330,682,682,223,219,0,219,219,161 0/2:7,0,10,0,0,0:17:99:383,404,654,0,250,220,404,654,250,654,404,654,250,654,654,404,654,250,654,654,654 0/3:23,0,0,19,0,0:42:99:704,773,1690,773,1690,1690,0,917,917,860,773,1690,1690,917,1690,773,1690,1690,917,1690,1690 0/0:43,0,0,0,0,0:43:51:0,51,1373,51,1373,1373,51,1373,1373,1373,51,1373,1373,1373,1373,51,1373,1373,1373,1373,1373 1/1:0,38,0,0,0,0:38:99:1639,114,0,1639,114,1640,1639,114,1640,1640,1639,114,1640,1640,1640,1639,114,1640,1640,1640,1640 1/4:0,9,0,0,13,0:22:99:1020,614,585,993,612,990,926,546,924,999,381,0,378,454,415,1000,620,998,968,423,1035 0/0:42,0,0,0,0,0:42:99:0,112,1625,112,1625,1625,112,1625,1625,1625,112,1625,1625,1625,1625,112,1625,1625,1625,1625,1625 0/4:28,0,0,0,18,0:46:99:652,736,1827,736,1827,1827,736,1827,1827,1827,0,1090,1090,1090,1036,736,1827,1827,1827,1090,1827 0/1:16,23,0,0,0,0:39:99:917,0,587,966,657,1622,966,657,1622,1622,966,657,1622,1622,1622,966,657,1622,1622,1622,1622 1/4:0,7,0,0,12,0:19:99:863,569,548,842,572,875,765,503,802,872,271,0,306,371,342,849,578,883,845,349,920 0/1:14,19,0,0,0,0:33:99:750,0,531,792,588,1380,792,588,1380,1380,792,588,1380,1380,1380,792,588,1380,1380,1380,1380
New vcf
##bcftools_viewVersion=1.21+htslib-1.21 ##bcftools_viewCommand=view -r NW_026622797.1:20902219-20902230 combined_genotype_output_10x.vcf.gz; Date=Thu Mar 27 14:51:25 2025 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT BB_WSU_973 BB_WSU_974 BB_WSU_975 BB_WSU_Adak BB_WSU_Cooke BB_WSU_Dodge BB_WSU_Frank BB_WSU_John BB_WSU_Oakley BB_WSU_Willow BB_WSU_Zuri NW_026622797.1 20902219 . G GCACA,GCACGCACA,GCACGCACACACA,GCACACA 1222.69 . AC=5,1,3,2;AF=0.227,0.045,0.136,0.091;AN=22;BaseQRankSum=-0.366;DP=84;ExcessHet=0.0343;FS=1.614;InbreedingCoeff=0.381;MLEAC=5,1,3,1;MLEAF=0.227,0.045,0.136,0.045;MQ=60;MQRankSum=0;QD=31.35;ReadPosRankSum=0;SOR=1.402 GT:AD:DP:GQ:PL 4/4:0,0,0,0,2:2:6:75,75,75,75,75,75,75,75,75,75,6,6,6,6,0 0/0:3,0,0,0,0:3:6:0,6,90,6,90,90,6,90,90,90,6,90,90,90,90 0/2:4,0,4,0,0:8:99:156,168,327,0,159,147,168,327,159,327,168,327,159,327,327 0/0:7,0,0,0,0:7:6:0,6,235,6,235,235,6,235,235,235,6,235,235,235,235 1/1:0,7,0,0,0:7:21:300,21,0,300,21,300,300,21,300,300,300,21,300,300,300 3/3:0,0,0,5,0:5:15:225,225,225,225,225,225,15,15,15,0,225,225,225,15,225 0/0:17,0,0,0,0:17:35:0,35,562,35,562,562,35,562,562,562,35,562,562,562,562 0/0:12,0,0,0,0:12:27:0,27,405,27,405,405,27,405,405,405,27,405,405,405,405 0/1:3,2,0,0,0:5:75:75,0,120,84,126,210,84,126,210,210,84,126,210,210,210 1/3:0,2,0,3,0:5:75:210,126,120,210,126,210,84,0,84,75,210,126,210,84,210 0/1:1,6,0,0,0:7:24:249,0,24,252,42,294,252,42,294,294,252,42,294,294,294
I don't understand the issue, can you provide more details. From your description it is not clear which bcftools command you are unhappy with and how were the two VCFs generated.
