Question: Bi-allelic SNP filtering
0
gravatar for nadiabeg.comsats
4 months ago by
nadiabeg.comsats0 wrote:

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?

ADD COMMENTlink modified 4 months ago by Pierre Lindenbaum128k • written 4 months ago by nadiabeg.comsats0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1172 users visited in the last hour