I'm using SAMTools to do some variant calling and I'd like to know how many supporting reads there are for the variant vs the consensus for the SNPs that it calls (like the indel lines). Is there a way to do this that I've missed? I want to use it as a filter on top of the mapping qualities.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Have a look at the samtools pileup format
See here: http://samtools.sourceforge.net/pileup.shtml
also, if you run samtools with the following command "samtools pileup -c -f <reference_sequence> in.bam" you will get for each position the support for consensus and for reference and some value that tells you the probability of a SNP at this position, I haven't read up on the details but I think that could be a good starting point.
Example Output:
dmel_mitochondrion_genome 2033 T T 10 0 0 3 ... AA>
You could try to extract your desired information from that.
Cheers,
Paul
"You are only young once, but you can stay immature indefinitely."
Latest Articles
Collapse
-
by seqadmin
The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...-
Channel: Articles
Yesterday, 07:48 AM -
-
by seqadmin
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
Channel: Articles
04-22-2024, 07:01 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Today, 06:57 AM
|
0 responses
9 views
0 likes
|
Last Post
by seqadmin
Today, 06:57 AM
|
||
Started by seqadmin, Yesterday, 07:17 AM
|
0 responses
14 views
0 likes
|
Last Post
by seqadmin
Yesterday, 07:17 AM
|
||
Started by seqadmin, 05-02-2024, 08:06 AM
|
0 responses
19 views
0 likes
|
Last Post
by seqadmin
05-02-2024, 08:06 AM
|
||
Started by seqadmin, 04-30-2024, 12:17 PM
|
0 responses
24 views
0 likes
|
Last Post
by seqadmin
04-30-2024, 12:17 PM
|
Comment