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Old 06-30-2015, 06:10 PM   #1
susanklein
Senior Member
 
Location: oceania

Join Date: Feb 2014
Posts: 115
Default finding the base at a position in a bam

Hi All,

I have seen some other threads on this subject, sorry I don't have the links. But none of them seem to resolve the problem. I am trying to do something very simple but no tools for bam files seem to have the facility. I have tried samtools and GATK to no avail.

All I need is to get the consensus read base at particular positions of the reference in a bam file. I am trying to check the state of SNPs from a particular bacterial SNP typing scheme in my NGS data. Not all of the positions will actually be a SNP, in which cae they have the same base as the reference, and I want that reported, so .vcf is no good to me.

Greatly appreciate any suggestions. I suppose I can just use samtools to make the vcf and then if a position is not listed then assume it is the reference base. I do find samtools almost impenetrable.. would this line be appropriate?

samtools mpileup -I -uBf ref.fasta 1_sorted.bam | bcftools view -bcg - > 1.bcf && bcftools view 1.bcf > 1.vcf

but I don't understand the output vcf file because it seems to have a '.' for the reference base and then the proper A T C or G for the 'alt' base(s).

Thanks for any help,

S.
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