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Old 02-10-2014, 08:19 PM   #1
variadevang
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Question Valid tools to use for Detecting SV/CNV in Whole Exome Data

I am working on whole exome data. i have 7 samples but no matching normal sample. i am to detect SV/CNV variant for these samples.
The sequencing platform is Illumina and i have BAM files ready for variant calling.
Are the tools PINDEL , BREAKSEQ and CNVnator Appropriate for Whole Exome Sequencing data without matching normal sample? i have tried ready the tool publication but they only refer to NGS data, not Exome Data Compatibility in Specific. If possible are any other tools available for WES Data without matching Normal!
NEED HELP!!!!!!!
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Old 02-11-2014, 05:17 AM   #2
TiborNagy
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If you have paired-end data, you can use BreakDancer without normal sample, but it is produce more false positives.
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Old 02-11-2014, 07:58 AM   #3
mchizar
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The DNASTAR Genomics Suite provides an assembler than can align multiple exomes on a desktop computer and produce BAM file output. The output BAM files can be analyzed in ArrayStar for variants, including CNV and do not require a "Normal" control. There are free 30-day demo you can request from their website.
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Old 02-11-2014, 11:56 AM   #4
m_two
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Look here: http://www.biostars.org/p/13807/

Breakdancer and Pindel will not really work because most breakpoints are not captured by exome capture sequencing. You will need an approach based on coverage and/or heterozygous SNP allele frequencies.

Last edited by m_two; 02-11-2014 at 11:59 AM.
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