I want to filter Snps from vcf file but i am confused that which parameter is good for SNPs filtering. In my vcf file i have found several condition that confused me. I show some of lines of vcf output.
FORMAT INFO **#CHROM POS ID REF ALT QUAL FILTER GT AD DP GQ PL AC AF AN INFO** Chr01 16434 . T A 32.77 . 0/1 53,6 59 61 61,0,2212 AC=1 0.500 2 BaseQRankSum=0.226 ClippingRankSum=0.000 DP=135 ExcessHet=3.0103 FS=1.850 MLEAC=1 MLEAF=0.500 MQ=32.25 MQRankSum=1.082 Chr01 103148 . C A 1017.77 . 0/1 25,3 55 99 1046,0,886 AC=1 0.500 2 BaseQRankSum=0.009 ClippingRankSum=0.000 DP=55 ExcessHet=3.0103 FS=0.000 MLEAC=1 MLEAF=0.500 MQ=60.20 MQRankSum=0.949 Chr01 15650 . C A 424.77 . 0/1 3,11 14 58 453,0,58 AC=1 0.500 2 BaseQRankSum=0.853 ClippingRankSum=0.000 DP=25 ExcessHet=3.0103 FS=0.000 MLEAC=1 MLEAF=0.500 MQ=49.38 MQRankSum=0.585 QD=30.34 ReadPosRankSum=1.479 SOR=0.760 Chr01 15651 . C A 424.77 . 0/1 3,11 14 58 453,0,58 AC=1 0.500 2 BaseQRankSum=0.763 ClippingRankSum=0.000 DP=25 ExcessHet=3.0103 FS=0.000 MLEAC=1 MLEAF=0.500 MQ=49.38 MQRankSum=0.585 QD=30.34 ReadPosRankSum=1.481 SOR=0.760
Now if you see this result, in the first line of result AD=53,6. It means 53 reads have same allele like reference and 6 reads have alternate allele. Is it right that i am saying. If not please tell me what is that?? If i am right then it is good snp ?? My second question is : There are some SNPs that have different DP in info and format column. For those what should i do?? And i read about this and i found that DP of info column is total reads depth and DP in format column is allelic depth. So it would be better to select the SNPs on the basis of allelic depth. Please explain me how should i select the SNPs ??
Thanks in advance