metrics

Steps:

1. Java 8 SE JDK http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html
2. Eclipse.org
3. terminal: git clone https://github.com/broadinstitute/picard
4. Eclipse: Import Project -> Gradle ->

Video:

https://drive.google.com/open?id=0B29M3sfdctitfktPOVluYjZfSEpzOUotWjY3M0ZGMDlRd2VySUo5RE5GSkptelpPWnhqcHc

Reference Sequence https://drive.google.com/file/d/0B29M3sfdctitQkRkVnA0cW9wbk0/view?usp=sharing

Data set: https://drive.google.com/folderview?id=0B29M3sfdctitSmprS1lFNnR6UUE&usp=sharing

NCBI test data: http://www.ncbi.nlm.nih.gov/tools/gbench/tutorial6/

Picard Tools: http://broadinstitute.github.io/picard/ https://github.com/broadinstitute/picard

HTSJDK: https://github.com/samtools/htsjdk

Средний файл "экзом" ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/NA12878/exome_alignment/NA12878.mapped.ILLUMINA.bwa.CEU.exome.20121211.bam размером 16 876 961 Kbytes (около 17 Гигабайт)

Маленький файл 19 хромосома ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/pilot2_high_cov_GRCh37_bams/data/NA12878/alignment/NA12878.chrom19.ILLUMINA.bwa.CEU.high_coverage.20100311.bam размером 6,3 Гбайт