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?

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