Samtools - pileup format question - "*" is a deletion

[cliff]

I am using SAMtools pileup to make indel and snp calls. In the read bases column (9th), there is a "*". Similar question can be found here

http://seqanswers.com/forums/showthread.php?t=3388&highlight=pileup

Here are some columns I picked from one position:

CHR POSITION Ref Base Genotype Reads Number
chr10 23172627 g S 31

Read Bases
c$t$c$a$c$c$.a,c,,**,,$,$,,$,,.,,,,,,,,,

My question is

I counted the allele frequency for each base and I found A has 2 reads, C has 5 reads, G has 21 reads, and T has 1 read. But the total number of reads here are 31. Since the two "*" represents two deletions, I should count "*" as which base?

Thanks

[Pepe]

Hi,

commas and periods represent reads with nucleotides that match the reference, that's why it says you have 31 of them.

I'm not sure about the **.

[nilshomer]

I am using SAMtools pileup to make indel and snp calls. In the read bases column (9th), there is a "*". Similar question can be found here

http://seqanswers.com/forums/showthread.php?t=3388&highlight=pileup

Here are some columns I picked from one position:

CHR POSITION Ref Base Genotype Reads Number
chr10 23172627 g S 31

Read Bases
c$t$c$a$c$c$.a,c,,**,,$,$,,$,,.,,,,,,,,,

My question is

I counted the allele frequency for each base and I found A has 2 reads, C has 5 reads, G has 21 reads, and T has 1 read. But the total number of reads here are 31. Since the two "*" represents two deletions, I should count "*" as which base?

Thanks

An easy way to determine the two reads with "*" would be to look at that position in a genome viewer (i.e. IGV or "samtools tview").

[sunhh]

Hi,
If you check the previous lines of this position "chr10 23172627", you will find some site that
has a deletion there. And this deletion makes a '*' label in the corresponding site here.
So, it means there are two reads supporting a deletion at this site.

Best.