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Complete newbie - can you help with LiftoverVCF?

flutabexflutabex Member
edited June 2018 in Ask the GATK team

Hi,
I'm completely new to linux and would like to use LiftoverVCF. I've tried with docker but kept getting stuck so have now installed Picard on the Linux Subsystem for Windows instead (Ubuntu 18.04). It seems to be running - I think! - but I can't tell if I'm doing it right. I get:


[email protected]:/c/users/flutabex/desktop$ java -jar picard.jar LiftoverVcf \

I=dels.vcf.gz \
O=lifted_over.vcf.gz \
CHAIN=gatk/hg38ToHg19.over.chain \
REJECT=rejected_variants.vcf \
R=gatk/ucsc.hg19.fasta.gz

17:08:19.129 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/c/users/flutabex/desktop/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Wed Jun 27 17:08:19 GMT 2018] LiftoverVcf INPUT=dels.vcf.gz OUTPUT=lifted_over.vcf.gz CHAIN=gatk/hg38ToHg19.over.chain REJECT=rejected_variants.vcf REFERENCE_SEQUENCE=gatk/ucsc.hg19.fasta.gz WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false RECOVER_SWAPPED_REF_ALT=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Wed Jun 27 17:08:19 GMT 2018] Executing as [email protected] on Linux 4.4.0-17134-Microsoft amd64; OpenJDK 64-Bit Server VM 10.0.1+10-Ubuntu-3ubuntu1; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.7-SNAPSHOT
INFO 2018-06-27 17:08:20 LiftoverVcf Loading up the target reference genome.
[Wed Jun 27 17:08:20 GMT 2018] picard.vcf.LiftoverVcf done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=201326592
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.NullPointerException
at picard.vcf.LiftoverVcf.doWork(LiftoverVcf.java:287)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:282)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)
[email protected]:/c/users/flutabex/desktop$


This seems to create empty files in my Picard folder called "I=dels.vcf", "O=lifted_over.vcf" etc.

Is that correct? If not then what should I do?

Sorry if that sounds really stupid - like I said, I've never used linux before.

Thank you

Answers

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