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AstraZeneca-NGS / VarDictJava

VarDict Java port
MIT License
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VCF merging between Mutect2 and VarDict output fail #382

Open lmanchon opened 1 year ago

lmanchon commented 1 year ago

java --jar $PICARD MergeVcfs I=${lib}"_Mutect2.vcf.gz" I=${lib}"_vardict.vcf.gz" O=${lib}"_picard_Variants.vcf.gz" INFO 2023-03-09 15:33:31 MergeVcfs

** NOTE: Picard's command line syntax is changing.

** For more information, please see: ** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)

** The command line looks like this in the new syntax:

** MergeVcfs -I GATK/HD829_S1_Mutect2.vcf.gz -I VARDICT/HD829_S1_vardict.vcf.gz -O SNV/HD829_S1_picard_Variants.vcf.gz

15:33:33.908 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/bioinfo/src/picard-tools/picard-2.20.7/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Thu Mar 09 15:33:34 CET 2023] MergeVcfs INPUT=[GATK/HD829_S1_Mutect2.vcf.gz, VARDICT/HD829_S1_vardict.vcf.gz] OUTPUT=SNV/HD829_S1_picard_Variants.vcf.gz VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Thu Mar 09 15:33:34 CET 2023] Executing as sassou@node107 on Linux 3.10.0-1160.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 15.0.1+9-18; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.20.7-SNAPSHOT [Thu Mar 09 15:33:34 CET 2023] picard.vcf.MergeVcfs done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=32440320 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Exception in thread "main" java.lang.IllegalArgumentException: The contig entries in input file VARDICT/HD829_S1_vardict.vcf.gz are not compatible with the others. at picard.vcf.MergeVcfs.doWork(MergeVcfs.java:189) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:305) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)

PolinaBevad commented 1 year ago

Hi @lmanchon, I believe it is not just VarDict issue. There is a difference between contig names used in both VCF files, please check that you used the same references for both of them.

lmanchon commented 1 year ago

right, i use recalibrated bam for Mutect2 and not recalibrated bam for Vardict. Do you think it's necessary to recalibrate bam file for Vardict ?