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Old 09-13-2013, 05:56 AM   #1
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Location: switzerland

Join Date: Aug 2011
Posts: 5
Default bwa-mem artifact with deletions


when I run bwa-mem with the options "-w 100 -O 5 -E 0.4" on paired end data I get the distribution of deletion sizes as shown in the attached image.

Can anybody give a hint where this spiky pattern comes from? It is not observed when aligning with bwa-aln or bowtie2, so it does not seem to be due to the sample. Any hint would be welcome.

best regards
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File Type: png frequency-vs-width-del.png (53.5 KB, 7 views)
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