geniusphil

## Hadoop For NGS Information

### Alignment
* [Spark BWA](https://github.com/citiususc/SparkBWA)
* [BigBWA](https://github.com/citiususc/BigBWA)

### Variant Calling
* [Vardoop](https://github.com/zcai/Vardoop)
* [gatk](https://github.com/broadinstitute/gatk)
### Annotation

geniusphil

library(ggplot2)
qual <- read.table("NA12878_QUAL.txt", header = FALSE)
hist(qual$V1,
    main="NA12878_QUAL",
    xlab="QUAL",
    xlim=c(0,4000),
    breaks=100)

geniusphil

# Check package
brew update
brew upgrade
brew install automake
brew install zlib
brew install pkg-config

# Download vcftools
git clone https://github.com/vcftools/vcftools.git
cd vcftools

geniusphil

Analysis flow

1. bwa mem alignment
2. samtools convert sam to bam
3. sambamba sort
4. sambamba mark duplication (markdup)
5. GATK Haplotype Caller
6. GATK GVCFs -> final vcf file
7. Annovar -- vcf to annovar input
8. Annovar -- table_annovar