BWA(PE)-CNVNator: Discover Copy Number Variations
Introduction
Map short reads to reference genome by using BWA, and call CNV with CNVnator_v0.2.2. This pipeline is only for hg19 [input:bam(sorted and indexed) output:CNVNator output formatfile,OPTION:bin size] notice:CNVNator considers N sequence located on start and end of chromosomes as a deletion.
| Input format | FASTQ (paired-end) |
| Library layout | Paired-end |
| Species | Human(hg19) |
| Execution time | About 3 hours. (27MB with 500K reads [45bp]) |
Results
CNV results (Original format)
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CNV results (GTF format)
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Pipeline history
Inputs
FASTQ-formatted dna sequence file (paired-end)
read1
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read2
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FASTQ Format Specification
Outputs
CNVnator original format
CNV results (Original format)
CNV results (GTF format)
GTF/GFF format output file
GTF format Specification
Options
Comments
Use case
Related information
Public
| BWA | (Original) | (NGS Surfer's wiki) |
| SAMtools | (Original) | (NGS Surfer's wiki) |
| CNVnator | (Original) | |