Counting mapped nucleotides in a bam file

[moriah]

Thanks for your help!

[ulz_peter]

you can set the criteria quite low and when using GATK (don't know for the others) it outputs the allele balance between the reference allele and the substituted allele.

It might miss some snps though if evidence is very low but I guess you do search variants with biological meaning and I guess he wouldn't miss those.

However, you would only get information of balance of 2 nucleotides. I don't think triallelic SNPs are supported yet.

Can't think of any other solution but maybe there's a fuction in bamtools/bedtools/samtools/picard that you might use

[moriah]

As far as I know snp calling won't always count a snp like one if there is not enough coverage or not sufficient quality score...
In addition, when I used a snp caller I got the consensus nucleotide and since I would like to see how much of each nucleotide covers specific position I am not sure if it fits...

Do you know how to overcome these issues using snp callers?
Thanks

[ulz_peter]

What about traditional SNP calling (for example using GATK). Is there any reason not to do it?

[moriah]

Thanks for your answer!

I saw the anomaly in the IGV for couple of genes and now I would like to check it in about 500 genes... so I have to find a way to do it automatically ...

[ulz_peter]

if it's just for some nucleotides and you need no autmoation:
IGV shows that information when you visualize it there's a coverage track. y moving the cursor over the relevant bar you'll get that information

[ulz_peter]

if it's just for some nucleotides and you need no autmoation:
IGV shows that information when you visualize it there's a coverage track. y moving the cursor over the relevant bar you'll get that information

[moriah]

Hi !

Is there a way to go over a sorted bam file and count how many different matches there are for a specific nucleotide - for example for a reference nucleotide T in position x - there are :12 T , 3A, 4C 0G..?\

Thanks ahead!