Question: VCF file REF Column outputs all 'N'
1
gravatar for mhasa006
3.8 years ago by
mhasa00650
United States
mhasa00650 wrote:

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

snp vcf • 1.5k views
ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by mhasa00650

'genome.fa' is a wrong REFerence.

ADD REPLYlink written 3.8 years ago by Pierre Lindenbaum122k

Thanks for the reply. here genome.fa is used for general purpose. I have the fasta file of the original genome. Is that what you meant? I also checked the positions in the original genome. There was no 'N' there. What could be the problem? 

ADD REPLYlink written 3.8 years ago by mhasa00650
Is the genome.fa the same file which was used for mapping in bam files? Maybe chromosome names are different?
ADD REPLYlink written 3.8 years ago by mkulecka310
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