Is it possible to have BWA align contigs to reference and have output visualised via IGV/Tablet with Gaps and SNPs highlighted?
I'm trying this strategy because I need to visualise alignment of 10-20 regions of the reference genome but don't have this regions in separated fasta files for other strains we want to identify SNPs/indels for some reference coordinates. All bacterial data is already assembled.
•
written
by
biotech
1 answer
Is it possible to have BWA align to contigs to the reference...
Yes
...and have output visualised via IGV/Tablet...
BAM format
...with Gaps and SNPs highlighted?
In IGV differences are colored by default. Indels are also marked. I assume Tablet does something similar, I've never used it.
Log in to answer this question.
-
Mapping a small number of contigs to a reference subsequence
written by alexandru.bologa.marian •
-
Tool to detect gene replacement in bacteria with NGS
written by kmyers2 •
-
Generate consensus from contig alignment to reference sequence
written by daewowo •
-
Why is eXpress producing strangely low counts?
written by bagi.m •
-
Extracting alignment coordinates from SAM file
written by dasakan •
-
Aligning Contigs of various Mtb strains to a reference genome and get the variants
written by Paul
-
can variants be called between two genomes?
written by Charles Yin
-
Extract consensus sequence from alignment
written by bird77 •
-
Bacterial SNP calling pipeline with SNP and indels confirmation
written by biotech
-
Bwa And Splicing Junctions
written by GPR
You may be able to use Mauve for this without doing alignments with bwa.