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Revision as of 20:54, 14 June 2014
, 20:54, 14 June 2014→BAM Files
=== BAM Files ===
=== BAM Files ===
Binary Sequence Alignment/Map (SAM) Format
* Maps reads to Chromosome/Position
* For a detailed explanation of the SAM/BAM format, see:
** SAM/BAM Spec: http://samtools.github.io/hts-specs/SAMv1.pdf
** Additional information I put together as I started working with SAM/BAM: [[SAM]]
Let's look at the BAMs (aligned reads that are ready for variant calling):
Let's look at the BAMs (aligned reads that are ready for variant calling):
ls ${OUT}/bams
ls ${OUT}/bams
[[File:GcalignOutBAMm.png|600px]]
[[File:GcalignOutBAMm.png|600px]]
Let's examine at the first 5 lines of the BAM file:
${GC}/bin/samtools view -h ${OUT}/bams/HG00551.recal.bam|head -n 5
; What is the first position in the BAM file?
<ul>
<div class="mw-collapsible mw-collapsed" style="width:200px">
<li>Answer</li>
<div class="mw-collapsible-content">
<ul>
<li>Chr 22, Pos: 16114122</li>
</ul>
[[File:BAM.png|750px]]
[[File:BAM.png|750px]]
</div>
</div>
</ul>
=== Quality Control Files ===
=== Quality Control Files ===
