Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Multisample vs single sample SNP calling

Hi,

I have performed multisample SNP calling and also single sample SNP calling for 8 individuals. Some of the variants detected by multi-sample SNP calling were absent in variants detected by single sample snp calling.

For example, Multisample SNP calling output:

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT BC210 BC212 BC214 BC217 BC219 BC226 BC229 BC230

chr1 389 . T G 178.50 . AC=6;AF=0.375;AN=16;BaseQRankSum=-0.775;DP=202;Dels=0.00;FS=26.344;HaplotypeScore=0.7725;MLEAC=6;MLEAF=0.375;MQ=12.37;MQ0=75;MQRankSum=-4.220;QD=1.08;ReadPosRankSum=0.073 GT:ADP:GQ:PL 0/1:21,21:42:35:35,0,116
0/0:11,7:18:9:0,9,68 0/1:13,5:18:18:18,0,58 0/1:8,14:21:39:39,0,59 0/1:16,16:32:59:66,0,59 0/1:14,7:20:43:43,0,85 0/1:10,20:29:19:21,0,19 0/0:9,9:18:6:0,6,44

Output from Individual SNP calling but merged into a single VCF file:

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT BC210 BC212 BC214 BC217 BC219 BC226 BC229 BC230

chr1 389 . T G 37.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.189;DP=33;Dels=0.00;FS=3.979;HaplotypeScore=2.9800;MLEAC=1;MLEAF=0.500;MQ0=12;MQ=12.44;MQRankSum=-1.474;QD=1.14;ReadPosRankSum=-0.794;SF=5 GT:GQP:PL:AD . .
. . 0/1:59:32:66,0,59:16,16 . . .

Here we can observe that the variant is present in only 1 individual from single sample SNP calling, whereas it is present in all the individuals with multi-sample SNP calling.

Could someone comment, which of these would be reliable results?

Best Answer

Answers

Sign In or Register to comment.