SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
IGV colors entire BAM file as inversions SrCardgage Bioinformatics 1 06-23-2015 06:56 AM
Which bam file is what I need to count reads? wmseq Bioinformatics 15 11-05-2013 12:34 PM
IGV - accessing BAM file from different server adrian Bioinformatics 2 07-16-2013 09:09 AM
loading bam file failure on IGV ykingh Bioinformatics 6 12-30-2011 01:58 PM
IGV bam file NicoBxl Bioinformatics 1 03-29-2011 05:24 AM

Reply
 
Thread Tools
Old 07-21-2015, 06:14 AM   #1
nottsbio
Junior Member
 
Location: Nottingham

Join Date: Jul 2015
Posts: 4
Question How to get deletion count from bam file in IGV?

I am trying to get a count of all bases, insertions and deletions from a bam file viewed in IGV genome viewer for each individual nucleotide. I can get the counts for the bases as a wig file (example shown below):

track type=wiggle_0
#Columns: Pos, Combined Strands A, Combined Strands C, Combined Strands G, Combined Strands T, Combined Strands N
variableStep chrom=E17F span=1
1 0 241 0 0 0
2 337 0 0 0 0
3 414 0 1 1 0
4 6 412 8 5 0
5 4 411 30 5 0
6 475 6 2 0 0
7 9 1 417 69 0

However, I also really want to get the count of deletions for each position. It is possible to get this count if you go through each position individually and write down the numbers (as shown in the image). But I was thinking surely there must be a way to do this in IGV? I have tried igvtools but it still doesn't give me a deletion count. Any guidance or other suggestions will be greatly appreciated!

Thanks
-T
Attached Images
File Type: png Deletion count.png (85.2 KB, 12 views)
nottsbio is offline   Reply With Quote
Old 07-21-2015, 06:26 AM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,479
Default

I'd be surprised if IGV included a way to do that, it would almost never be used. You could either parse the output of "samtools mpileup" or just directly use a variant caller, as applicable.
dpryan is offline   Reply With Quote
Old 07-22-2015, 03:43 AM   #3
nottsbio
Junior Member
 
Location: Nottingham

Join Date: Jul 2015
Posts: 4
Default

Quote:
Originally Posted by dpryan View Post
I'd be surprised if IGV included a way to do that, it would almost never be used. You could either parse the output of "samtools mpileup" or just directly use a variant caller, as applicable.
Thanks for the suggestions! I'm not very experienced in the bioinformatics, would you be able to clarify what you mean by these? I'm not sure how I would parse the output of mpileup. This is what I am trying with it but I am unsure what options to use to get the output I want.

$ samtools mpileup -f reference.fasta -Q 13 input.sorted.bam -o output.txt

Also directly using a variant caller, does that mean calling variants from my bam file - what sort of output can I get from that?

Sorry for all the questions and thank you for your suggestions, I really appreciate it!!
nottsbio is offline   Reply With Quote
Old 07-22-2015, 03:45 AM   #4
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,479
Default

Maybe we should go about this in a different way. What is your biological goal? That is, what is the biological question that you're trying to answer by doing this?
dpryan is offline   Reply With Quote
Old 07-22-2015, 03:50 AM   #5
nottsbio
Junior Member
 
Location: Nottingham

Join Date: Jul 2015
Posts: 4
Default

I have a mutant sample with a deletion and I want to see if the deletion count in this region is significantly higher compared to the wild type (using a new genome sequencer - so I want to see if it can detect deletions). But I want to get the base (ACGT, insertion, deletion) counts for every position so I can tell if the detected deletion is significant or if the sequencing device just has a high error rate. Hope that makes more sense!
nottsbio is offline   Reply With Quote
Old 07-22-2015, 04:01 AM   #6
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,479
Default

Right, so you want to call variants between the mutant and wild-type samples, paying attention to only a small region. Just use a variant caller and ensure that it finds the deletion in the mutant but not wild-type sample. I'd recommend GATK's haplotype caller, since it enables joint variant calling. If you really wanted, you could compare the genotyping probabilities between the samples (it's one of the fields in the VCF file produced). This assumes that the deletion isn't very large, in which case other tools targeted specifically toward finding large deletions might give better results.
dpryan is offline   Reply With Quote
Old 07-22-2015, 04:08 AM   #7
nottsbio
Junior Member
 
Location: Nottingham

Join Date: Jul 2015
Posts: 4
Default

Thank you for your help, I will try this!
nottsbio is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 05:32 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO