GATK

Variant calling을 위해서 GATK를 사용해 보았다.

 

공식 : https://gatk.broadinstitute.org/hc/en-us

다운로드  : https://github.com/broadinstitute/gatk/releases

$ wget https://github.com/broadinstitute/gatk/releases/download/4.1.8.1/gatk-4.1.8.1.zip
$ unzip gatk-4.1.8.1.zip
$ cd gatk-4.1.8.1
$ ./gatk

압축을 풀고 나서 설치과정 없이 바로 사용 가능하다.

 

준비과정으로 reference fasta file의 dictionary만드는 과정이 필요하다.

$ samtools faidx hg37.fa # generate index file
$ gatk CreateSequenceDictionary -R hg37.fa

 

Variant calling

$ gatk HaplotypeCaller -R hg37.fa -I input.bam -O output.vcf.gz --read-filter OverclippedReadFilter --native-pair-hmm-threads 8
or 
$ gatk HaplotypeCaller \
   -R hg37.fa \
   -I input.bam \
   -O output.vcf.gz \
   --read-filter OverclippedReadFilter \
   --native-pair-hmm-threads 8

다양한 옵션들은 아래 링크를 참고하면 된다.

https://gatk.broadinstitute.org/hc/en-us/articles/360036897532-HaplotypeCaller

https://gatk.broadinstitute.org/hc/en-us/articles/360035531892-GATK4-command-line-syntax

 

RAM VIRT~36.7GB RES~ 1990MB

$ find *.bam | awk -F. '{print $1}' | while read line;do echo "gatk HaplotypeCaller -R hg37.fa -I ${line}.bam -O ${line}.vcf.gz --read-filter OverclippedReadFilter";done | parallel --bar -j5 {}

 

Coverage - Read depth metrics

https://gatk.broadinstitute.org/hc/en-us/articles/360041851491-DepthOfCoverage-BETA-

$ gatk \
   DepthOfCoverage \
   -R reference.fasta \
   -O file_name_base \
   -I input_bams.list \
   [-geneList refSeq.sorted.refseq] \
   [-pt readgroup] \
   [-ct 4 -ct 6 -ct 10] \
   [-L my_capture_genes.interval_list]

* The file extension of 'input_bams.list' must be '.list'.

 

Funcotator for annotation

https://gatk.broadinstitute.org/hc/en-us/articles/360035889931-Funcotator-Information-and-Tutorial

# A VCF instantiation of the Funcotator tool looks like this:
$ ./gatk Funcotator \
     --variant variants.vcf \
     --reference Homo_sapiens_assembly19.fasta \
     --ref-version hg19 \
     --data-sources-path funcotator_dataSources.v1.2.20180329 \
     --output variants.funcotated.vcf \
     --output-file-format VCF

http://ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/funcotator/

 

 

INFO

QUAL/AD = 1063.77/31 = 34.32 = QD