igvtools count - how do I get it to show insertion and deletion count

Question

[kwgsmith]

Hello,

I am running the command:

igvtools count -w 1 --bases --query chr1:1326-1338 --minMapQuality 30 input.bam output.wig ref.fa

I get the correct number of A,C,G,T,N base counts as seen in IGV. However, I also need the number of insertions and deletions. They are shown in the GUI version, but I am unsure after looking at the documentation for igvtools count how to have it return these two values. I'm sure it's something simple I'm missing.

Any help you can provide would be appreciated.

Thanks!

Answer 1

[dariober]

I don't know about igvtools but have a look at pysamstats. See also these threads Calculate The Frequency Of Nucleotides At Each Position In An Mpileup File and Nucletotide distribution, at each position, in a .sam/.bam file ?

[kwgsmith]

I've tried pysamstats and it gives the incorrect (according to IGV) number of insertions and deletions. Oddly though it gives the same insertions and deletions that my perl script, which I wrote after I tried pileup2indel and pysamstats and before I ran across igvtools, calculates.

I tried to talk to the creator of pysamstats, but unfortunately I couldn't share my data with him or come up with something similar enough that he could help.

I've also looked at mpileup, but it will not do everything I want it to do, or at least that is my understanding after talking with someone much more knowledgeable in my lab.

Thanks for the reply though!

Answer 2

[Titus]

Hi , I m using igvtools count and if i had this options --strands read i have INDEL and the information number of count in foward and reverse ! It looks like the information you want to :)

And just a few thinks when i use the command i got all the information right (number of A,C,G,T,DEL,INS) except for INS foward information witch is always equal to 0 . Is it a bug ?

Best regards

Tristan