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Revision as of 19:39, 9 December 2014
, 19:39, 9 December 2014→Sequnce Alignment Files: BAM Files and Index Files
If you want to check if you still have the bam index file, run
If you want to check if you still have the bam index file, run
head ${OUT}/bam.index
head ${OUT}/bam.list
<ul>
<ul>
<li>View Results</li>
<li>View Results</li>
<div class="mw-collapsible-content" style="width:800px">
<div class="mw-collapsible-content" style="width:800px">
HG00641 ALL /net/seqshop-server/hmkang/out/bams/HG00641.recal.bam
HG00641 /net/seqshop-server/home/hmkang/out/bams/HG00641.recal.bam
HG00640 ALL /net/seqshop-server/hmkang/out/bams/HG00640.recal.bam
HG00640 /net/seqshop-server/home/hmkang/out/bams/HG00640.recal.bam
HG00551 ALL /net/seqshop-server/hmkang/out/bams/HG00551.recal.bam
HG00551 /net/seqshop-server/home/hmkang/out/bams/HG00551.recal.bam
HG00553 ALL /net/seqshop-server/hmkang/out/bams/HG00553.recal.bam
HG00553 /net/seqshop-server/home/hmkang/out/bams/HG00553.recal.bam
HG00554 ALL bams/HG00554.recal.bam
HG00554 bams/HG00554.recal.bam
HG00637 ALL bams/HG00637.recal.bam
HG00637 bams/HG00637.recal.bam
HG00638 ALL bams/HG00638.recal.bam
HG00638 bams/HG00638.recal.bam
HG00734 ALL bams/HG00734.recal.bam
HG00734 bams/HG00734.recal.bam
HG00736 ALL bams/HG00736.recal.bam
HG00736 bams/HG00736.recal.bam
HG00737 ALL bams/HG00737.recal.bam
HG00737 bams/HG00737.recal.bam
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</div>
</div>
Also, make sure that you have only 62 samples (you did not append new files twice)
Also, make sure that you have only 62 samples (you did not append new files twice)
wc -l ${OUT}/bam.index
wc -l ${OUT}/bam.list
Your expected output is similar to this.
Your expected output is similar to this.
62 /net/seqshop-server/hmkang/out/bam.index
62 /net/seqshop-server/hmkang/out/bam.list
=== Reference Files ===
=== Reference Files ===
