Identify and count gaps in sam/bam files
Is there a straightforward way to identify and tally the gaps in a sam/bam file created by bwa? A glance at the mapping using IGV suggests that there are virtually no gaps in a mapping that I recently generated, which is problematic. I would like to know if there are any gaps at all.
Is there some way to doing this using a samtools function, or perhaps some other application?
• 1,426 views
•
link
updated
by
Mark
•
written
by
shpak.max •
•
written
by
shpak.max •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Correcting a lack of gaps in bwa aln mapping of unpaired reads
written by shpak.max •
-
Best way to deal with overlapping read names in merged BAM files
written by shpak.max •
-
Finding exactly where reads map from SAM
written by Sisyphus •
-
Treating forward and reverse reads independently in BWA
written by shpak.max •
-
bamdst gives error "EOF marker is absent. The input is probably truncated."
written by shpak.max •
-
Detect Transgene Insertion Site using SAM format
written by kspata
-
Kallisto pseudobam to IGV
written by mac
-
SAM to BAM conversion error
written by jitendoshi2006 •
-
Weird alignments in amplicon sequencing
written by kulvait
-
How To Tell How Well A Sam File Was Mapped
written by Applet •
And with gap, you mean a portion of the genome that has no aligned reads?
I'm referring to gaps corresponding to indels.
You need to do variant calling.
samtools depth -aashould do what you're after. It outputs a tab de limited file. Then use your favorite tool to compute visualize.