counts in coverage are different

[aparna p]

Hi Jim,

I am parsing mpileup format lately using :
-Ds -BQq0 and by supplying bed and fasta referene file.
I have attached my sample mpileup file here for your reference.

and found that the counts displayed on IGV coverage at many positions are slightly different to what I am getting.

For ex:
Chr    Pos    Ref    Alt    Strnd    AF    AFO    ARO    size    Type    AvgQscore    AvgMAPQ    FRO    RRO    DP
chr7    55233019    A    *    +    2    2    0    1    DEL    29    88        5896    6465    12603
chr7    55233019    A    C    +    1292    1292    0    1    INS    25    13        5896    6465    12603
chr7    55233019    A    G    -    7    0    7    1    INS    25    13        5896    6465    12603
chr7    55233019    A    GC    +    1    1    0    2    INS    25    13        5896    6465    12603
chr7    55233019    A    T    +    1    1    0    1    INS    25    13        5896    6465    12603
chr7    55233019    A    C    +    70    70    0    1    SNP    24    88        5896    6465    12603
chr7    55233019    A    C    -    76    70    6    1    SNP    284    1071        5896    6465    12603
chr7    55233019    A    G    +    1    1    0    1    SNP    29    93        5896    6465    12603
chr7    55233019    A    G    -    3    1    2    1    SNP    14    73        5896    6465    12603

and IGV 2.3.32.37 shows:

Total count: 12601
A : 12361 (98%, 5896+, 6465- )
C : 223 (2%, 219+, 4- )
G : 16 (0%, 4+, 12- )
T : 1 (0%, 1+, 0- )
N : 0
---------------
DEL: 2
INS: 1342

I think mpileup is counting deletions aswell towards total DP, which I can ignore,but overall counts dont tally. I am getting 1301 Insertions and 150 SNPs.

How are you getting the counts in the coverage track?
Thanks for looking in to it.

Aparna

[Jim Robinson]

We simply count,  mpileup does something slightly different.    I'm not an mpileup expert,  you'll need to ask on the samtools list to get details, or consult the mpileup documentation.

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