I'm using samtools to look for SNPs with ultradeep (>18,000X) coverage. For some reason samtools and bcftools does not call some of the SNPs.
For example, at position 16215, IGV gives me:
Total count: 18522
A: 17030 (92%, 8124+, 8906-)
C: 0
G: 1516 (8%, 861+, 655-)
T: 5 (0%, 4+, 1-)
N:1 (0%, 1+, 0-)
Sam/bcftools should be making a SNP call at position 16215 but is not. Also, the first two counts in DP4 almost agree between bcftools and IGV, but the third and fourth do not. The sequences are quality trimmed and the reads containing the A allele are not of low quality.
Anyone know why? Thanks.
Code:
gi|251831106|ref|NC_012920.1| 16125 . G . 99 . DP=18552;AF1=0;CI95=1.5,0;DP4=832,646,0,1;MQ=35;PV4=0.44,0.14,1,1 PL 0 gi|251831106|ref|NC_012920.1| 16126 . T C 99 . DP=18770;AF1=1;CI95=1,1;DP4=28,21,777,596;MQ=35;PV4=1,0,0.00042,0.28 PL 219,255,0
Total count: 18522
A: 17030 (92%, 8124+, 8906-)
C: 0
G: 1516 (8%, 861+, 655-)
T: 5 (0%, 4+, 1-)
N:1 (0%, 1+, 0-)
Sam/bcftools should be making a SNP call at position 16215 but is not. Also, the first two counts in DP4 almost agree between bcftools and IGV, but the third and fourth do not. The sequences are quality trimmed and the reads containing the A allele are not of low quality.
Anyone know why? Thanks.
Comment