I am doing SNP calling using samtools. The way I'm doing is following.
- I had a .bam file that contains information for all chromosome together.
- I extracted information for each chromosome and make separate bam file for each chromosome.
- I made a snpcall using mpileup. Separately each chromosome with the whole genome. Following is the result for Chromosome 1. Below is a section of my output.
GeneDB|Pf3D7_01_v3 107 . N G 68.5 . DP=4;VDB=9.421102e-03;AF1=1;AC1=2;DP4=0,0,4,0;MQ=58;FQ=-39 GT:PL:GQ 1/1:101,12,0:21
GeneDB|Pf3D7_01_v3 108 . N A 148 . DP=12;VDB=3.982228e-05;AF1=1;AC1=2;DP4=0,0,12,0;MQ=54;FQ=-63 GT:PL:GQ 1/1:181,36,0:69
GeneDB|Pf3D7_01_v3 109 . N A 152 . DP=13;VDB=3.441712e-05;AF1=1;AC1=2;DP4=0,0,13,0;MQ=54;FQ=-66 GT:PL:GQ 1/1:185,39,0:75
All the REF values are 'N'. what could be the problem?
I used the following command:
samtools mpileup -uf genome.fa in.bam | bcftools view -bvcg - > out.raw.bcf