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