Bi-allelic SNP filtering
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15 months ago

Hi all, I am trying to get bi-allelic snps from my vcf file. I have a combined vcf file for 8 samples having tetraploid genomes. For getting bi-allelic markers I am using following command. bcftools view -m2 -M2 -v snps input.vcf.gz

After filtering I am getting some weird marker entries as well such as,

Chr01   431     .       CTTTTTTGGTGA    GTTTTTTGGTGA    40.56   AB=0.166667;ABP=43.5445;AC=3;AF=0.0833333 ;TYPE=snp;technology.ILLUMINA=1   GT:AD:AO:DP:QA:QR:RO    0/0/0/0:16,0:0:29:0:585:16      0/0/0/0:18,0:0:20:0:683:18      0/0/0/0:10,0:0:11:0:375:10      0/0/0/0:7,0:0:10:0:276:7        0/0/0/0:9,0:0:10:0:328:9        0/0/0/1:9,3:3:14:113:342:9      0/0/0/1:12,3:3:18:104:425:12    0/0/0/1:7,1:1:10:32:263:7       0/0/0/0:3,0:0:3:0:105:3

Chr01   1407    .       TTAC    TTAT    421.02  .       AB=0.0991561;ABP=664.531;AC=9;AF=0.25 TYPE=snp;technology.ILLUMINA=1 GT:AD:AO:DP:QA:QR:RO    0/0/0/1:59,5:5:68:158:2112:59   0/0/0/1:68,7:7:76:255:2543:68
   0/0/0/1:24,7:7:36:263:901:24    0/0/0/1:74,4:4:92:135:2927:74   0/0/0/1:41,5:5:48:167:1569:41   0/0/0/1:34,10:10:47:349:1187:34 0/0/0/1:44,3:3:51:97:1634:44    0/0/0/1:16,2:2:22:74:568:16     0/0/0/1:27,4:4:34:156:1028:27

Chr01   3006    .       CATTTTTTCCA     CATTTTTGCCA     20.57   .  AB=0.115385;ABP=69.8248;AC=4;AF=0.111111 YPE=snp;technology.ILLUMINA=1    GT:AD:AO:DP:QA:QR:RO    0/0/0/1:16,3:3:22:123:593:16    0/0/0/0:9,0:0:10:0:329:9        0/0/0/1:18,1:1:20:41:670:18     0/0/0/1:2,1:1:5:41:79:2 0/0/0/0:12,0:0:14:0:454:12      0/0/0/1:4,1:1:5:37:149:4        0/0/0/0:17,0:0:20:0:643:17      0/0/0/0:11,1:1:12:11:399:11     0/0/0/0:8,0:0:12:0:286:8

Chr01   7324    .       TTTT    TTTC    2751.9  .       AB=0.392027;ABP=33.4903;AC=15;AF=0.416667;TYPE=snp;technology.ILLUMINA=1    GT:AD:AO:DP:QA:QR:RO    0/0/0/1:24,6:6:31:188:893:24    0/0/0/1:18,6:6:26:245:632:18    0/0/1/1:8,5:5:14:143:292:8      0/0/1/1:26,36:36:69:1358:959:26 0/0/0/1:20,12:12:34:395:738:20  0/0/1/1:13,10:10:23:377:485:13  0/0/1/1:14,10:10:26:365:525:14  0/0/1/1:24,15:15:41:529:872:24  0/0/1/1:16,18:18:37:676:590:16

These variants have high quality scores compared to simple A/T and C/G variants. My questions are i) Are the aforementioned variants are bi-allelic and bcf-tools does filtering for bi-allelic variants as well?

bcftools bi-allelic snps tetraploid genome • 441 views
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