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Old 09-21-2015, 02:35 AM   #1
mandar.bobade60
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Location: India

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Default Structural variation detection from Exome-seq single-end data

Hi,
I am having single-end sequencing data from ION TORRENT which further subjected to reference alignment using Bowtie2. After that I ran GATK pipeline for SNP detection. Now I want to detect structural variants from sam/bam file obtained from GATK. I did read Delly/Lumpy algorithm where they have mentioned it is for paired-end, mate-paired, and split alignment. For Bowtie2 I couldn't find split alignment option, but BWA has this option. Following two questions pertaining to same:
1) Can I still find structural variants using current bam/sam file obtained from Bowtie2 and GATK?

2) If I were to find structural variants using single end data, Is it possible to find with single-end data?

3) Which are best suited tools for SV detection for single-end data?

Regards,
Mandar
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