How to count indels called by SAMtools

[yuanzhi]

I have the following pileup file called by SAMtools. I want to count the number of indels in this region. Should I just simply count the total number of "*" present in the 3rd column?

chr1    241     *       */+A    383     383     20      365     *       +A      339     24      2       7       44
chr1    352     *       */+A    2266    2266    24      278     *       +A      218     59      1       19      51
chr1    389     *       */-c    480     480     20      364     *       -c      345     17      2       0       0
chr1    3280    *       */+GAGA 1839    1839    18      185     *       +GAGA   157     28      0       0       0
chr1    4793    A       G       20      20      27      139     .G,gg.G.G,G,G.Gg.,,G.,g,Gg,,CGg.GG.,G,G,ggG.G.g..G,..,G.ggG,.GgG.g,GG,....G.G...,GG.G,,.gG.,G,.G.Gg..,,g.GG..G.GG,G.G.g,gG,.g.GG,.G.ggg.gG.       F?G/B8>3BCBGGAD?CBG5GGAGEGHF%FG7=H@G=G1=GBBDH<B:B>D;E3B;ACGE3HE1EGE?GEA>=FD;HBH:EDHGB/4ABGEGHDAG.HA7G=6BHHG;H9HGGB>GGG.5=;4HE=B?4AH@@CCG@;@
chr1    18454   *       +GG/*   591     832     26      28      +GG     *       3       24      1       0       0
chr1    20730   *       */-ct   810     810     32      120     *       -ct     105     4       11      11      96

[drio]

Yes, you are fine counting '*'.

[yuanzhi]

Thanks, drio.

But how about if some insertions or deletions have more than one base? If I just count each "*" as an INDEL, does that mean I assume each INDEL is just one base long.

I often see some deletions are more than 10 bp. Maybe I should count those "*" present in consecutive bases as one INDEL?

[drio]

Look at these examples:

chr17   597711  *       */-tgtgagccagga 182     182     20      38      *       -tgtgagccagga   35      3       0       0       0
chr17   142646  *       */+AAAC 185     185     31      45      *       +AAAC   41      4       0       0       0

First, an heterozygous deletion (12bp). Second another heterozygous insertion (4bp).