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Revision as of 14:16, 15 June 2014
, 14:16, 15 June 2014→BAM Files
[[File:GcalignOutBAMm.png|600px]]
[[File:GcalignOutBAMm.png|600px]]
Let's examine at the first 5 lines of the BAM file:
Let's examine at the first 5 lines of the BAM file using [http://samtools.sourceforge.net/samtools.shtml#3 samtools view]:
${GC}/bin/samtools view -h ${OUT}/bams/HG00551.recal.bam|head -n 5
${GC}/bin/samtools view -h ${OUT}/bams/HG00551.recal.bam|head -n 5
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==== Accessing BAMs by Position ====
BAM's are so big, what if we want to see a position part way through the file?
:[http://samtools.sourceforge.net/samtools.shtml#3 samtools] has an option for that.
Add a region to the view command we used above. Let's find all reads that overlap positions 36907000-36907005:
${GC}/bin/samtools view -h ${OUT}/bams/HG00551.recal.bam 22:36907000-36907005
* Just a few reads.
Let's visualize what reads in that area look like using samtools tview:
${GC}/bin/samtools tview ${OUT}/bams/HG00551.recal.bam ${REF}/human.g1k.v37.chr22.fa
* Type ‘g’
** Type 22:36907000
* Type ‘n’ to color by nucleotide
* Use the arrow keys to move around and look at the area.
Understanding the syntax:
* '.' : match to the reference on the forward strand
* ',' : match to the reference on the reverse strand
* ACGTN : mismatch to reference on the forward strand
* acgtn : mismatch to reference on the reverse strand
; Do you see anything interesting?
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*Screenshot
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<li>We will have to remember this region when we run snpcall to see what it says.</li>
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[[File:tview.png|750px]]
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Other commands:
* Type '?' for a help screen
* Type 'q' to quit tview
== Logging Off ==
== Logging Off ==
