[GATK] GATK 오류 - "Problem detecting index type" 해결법

안녕하세요

한주현 입니다


오늘은 GATK 오류메시지인 "Problem detecting index type" 해결법에 대해 알아보겠습니다

현상

$ java -Xmx40g -Djava.io.tmpdir=/tmp -jar GenomeAnalysisTK.jar  -T GenotypeGVCFs  -R ucsc.hg19.fasta --variant multicall.gvcf.list --out rawVariants.vcf
INFO  10:52:58,657 HelpFormatter - -----------------------------------------------------------------------------------------
INFO  10:52:58,659 HelpFormatter - The Genome Analysis Toolkit (GATK)
...

INFO  10:52:58,669 HelpFormatter - Date/Time: 2017/10/16 10:52:58
INFO  10:52:58,669 HelpFormatter - -----------------------------------------------------------------------------------------
INFO  10:52:58,669 HelpFormatter - -----------------------------------------------------------------------------------------
WARN  10:52:58,680 CommandLineExecutable - License has expired, please contact Appistry to renew.
INFO  10:52:59,230 GenomeAnalysisEngine - Strictness is SILENT
INFO  10:52:59,306 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website for extensive documentation and answers to
##### ERROR commonly asked questions http://gatkdocs.appistry.com/
##### ERROR
##### ERROR MESSAGE: Problem detecting index type
##### ERROR ------------------------------------------------------------------------------------------

오류메시지의 bold와 색깔은 원래는 안 나오지만 가시성을 위해 칠해봤습니다 ㅎㅎ

해결방법

vcf의 index 파일 (vcf.idx)이 잘못되어 생긴 현상으로,

간단히 vcf index 파일을 삭제해주시고 다시 실행하면 됩니다 ㅎㅎ;

생각보다 해결방법이 간단하죠? ㅎㅎ

그럼 다음에 또 만나요~

참고 URL

https://gatkforums.broadinstitute.org/gatk/discussion/4831/what-does-this-error-mean-problem-detecting-index-type