confused about the pileup data

[MissDona]

hi all,
I'm quite confused with the samtools mpileup result of some reads, such as:
,..^+,^>,
.+2CT^>.^!,
.*.*^>,
what does ">", "<", "^+", "^>", "*" means?
thanks alot!

[sBeier]

It looks a bit as if you opened the binary version of the result file (bcf). If so, convert it to vcf using the vcftools. If this is not the case, could you post some lines of the result file? Without context it is hard to guess.

[MissDona]

I think I've figured out most of them with http://www.biostars.org/p/8566/,
but yet cannot figure out the differenct between "^]." and "^!."

[MissDona]

thanks sBeier,
but this is not bcf file, this is the fifth column(that is, the read list column of samtools mpileup result)
with a few full lines here:
1 10086 A 16 ..........,,..., ?EBCCB*BCB?C9B@< F4>>>>"!>>!>>+-!
1 10087 A 16 ..........,,..., ?EEDF93<DD=@@<D4 F4>>>>"!>>!>>+-!
1 10088 C 16 ..........,,..., DEGFFB>ACFEFADEF F4>>>>"!>>!>>+-!

[MissDona]

I think I figured out them all, the content in the parentheses of "^()" means the mapping quality of the read.

[sBeier]

Usually in the comment lines at the beginning of VCF, all of the columns are explained. Because you can have specific columns for many tools that generate VCFs