原文件如下：
直接使用gatk 的 IndexFeatureFile 参数：
#gatk IndexFeatureFile -F vcf_file
$ gatk IndexFeatureFile -F Mills_and_1000G_gold_standard.indels.hg38.vcf
Using GATK jar /share_data/wujm/software/gatk-4.1.4.0/gatk-package-4.1.4.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /share_data/wujm/software/gatk-4.1.4.0/gatk-package-4.1.4.0-local.jar IndexFeatureFile -F Mills_and_1000G_gold_standard.indels.hg38.vcf
13:23:38.650 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/share_data/wujm/software/gatk-4.1.4.0/gatk-package-4.1.4.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Dec 06, 2021 1:23:38 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
13:23:38.875 INFO IndexFeatureFile - ------------------------------------------------------------
13:23:38.875 INFO IndexFeatureFile - The Genome Analysis Toolkit (GATK) v4.1.4.0
13:23:38.875 INFO IndexFeatureFile - For support and documentation go to https://software.broadinstitute.org/gatk/
13:23:38.875 INFO IndexFeatureFile - Executing as wujianming@pang on Linux v3.10.0-957.el7.x86_64 amd64
13:23:38.876 INFO IndexFeatureFile - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_152-release-1056-b12
13:23:38.876 INFO IndexFeatureFile - Start Date/Time: 2021年12月6日 下午01时23分38秒
13:23:38.876 INFO IndexFeatureFile - ------------------------------------------------------------
13:23:38.876 INFO IndexFeatureFile - ------------------------------------------------------------
13:23:38.876 INFO IndexFeatureFile - HTSJDK Version: 2.20.3
13:23:38.876 INFO IndexFeatureFile - Picard Version: 2.21.1
13:23:38.876 INFO IndexFeatureFile - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:23:38.876 INFO IndexFeatureFile - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:23:38.876 INFO IndexFeatureFile - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:23:38.876 INFO IndexFeatureFile - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:23:38.876 INFO IndexFeatureFile - Deflater: IntelDeflater
13:23:38.877 INFO IndexFeatureFile - Inflater: IntelInflater
13:23:38.877 INFO IndexFeatureFile - GCS max retries/reopens: 20
13:23:38.877 INFO IndexFeatureFile - Requester pays: disabled
13:23:38.877 INFO IndexFeatureFile - Initializing engine
13:23:38.877 INFO IndexFeatureFile - Done initializing engine
13:23:39.092 INFO FeatureManager - Using codec VCFCodec to read file file:///share_data/wujm/Config/reference/hg38/Mills_and_1000G_gold_standard.indels.hg38.vcf
13:23:39.138 INFO ProgressMeter - Starting traversal
13:23:39.138 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
13:23:41.420 INFO ProgressMeter - chrX:152403569 0.0 1271815 33454142.9
13:23:41.421 INFO ProgressMeter - Traversal complete. Processed 1271815 total records in 0.0 minutes.
13:23:41.594 INFO IndexFeatureFile - Successfully wrote index to /share_data/wujm/Config/reference/hg38/Mills_and_1000G_gold_standard.indels.hg38.vcf.idx
13:23:41.594 INFO IndexFeatureFile - Shutting down engine
[2021年12月6日 下午01时23分41秒] org.broadinstitute.hellbender.tools.IndexFeatureFile done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=2573729792
Tool returned:
/share_data/wujm/Config/reference/hg38/Mills_and_1000G_gold_standard.indels.hg38.vcf.idx---------- 如果这篇文章对您有帮助，请您随手点个赞，谢谢啦~~~~ ---------