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LiftOverVcf Not Working

Hello:

Getting an error with LiftoverVcf. The Output Seems to have most of the information about my Java and such. Including all the other relevant information i could find - chain file i am using, header of VCF, and a sample entry.

Hopefully that is sufficient. If there is anything else i can provide, definitely let me know.

Also, thank-you for providing such an incredible free resource!

Chain File
http://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz

Command Line:
gatk LiftoverVcf --INPUT 55001705017931A.raw.snp.vcf --OUTPUT 55001705017931A_hg38.raw.snp.vcf --CHAIN hg19ToHg38.over.chain --REJECT 55001705017931A_hg38_reject.raw.snp.vcf --REFERENCE_SEQUENCE hg38.fa

Output
Using GATK jar /mnt/e/Various/Genome/gatk-4.0.4.0/gatk-package-4.0.4.0-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 /mnt/e/Various/Genome/gatk-4.0.4.0/gatk-package-4.0.4.0-local.jar LiftoverVcf --INPUT 55001705017931A.raw.snp.vcf --OUTPUT 55001705017931A_hg38.raw.snp.vcf --CHAIN hg19ToHg38.over.chain --REJECT 55001705017931A_hg38_reject.raw.snp.vcf --REFERENCE_SEQUENCE hg38.fa
17:11:16.639 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/mnt/e/Various/Genome/gatk-4.0.4.0/gatk-package-4.0.4.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Sun May 06 17:11:16 GMT 2018] LiftoverVcf --INPUT 55001705017931A.raw.snp.vcf --OUTPUT 55001705017931A_hg38.raw.snp.vcf --CHAIN hg19ToHg38.over.chain --REJECT 55001705017931A_hg38_reject.raw.snp.vcf --REFERENCE_SEQUENCE hg38.fa --WARN_ON_MISSING_CONTIG false --LOG_FAILED_INTERVALS true --WRITE_ORIGINAL_POSITION false --LIFTOVER_MIN_MATCH 1.0 --ALLOW_MISSING_FIELDS_IN_HEADER false --TAGS_TO_REVERSE AF --TAGS_TO_DROP MAX_AF --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Sun May 06 17:11:16 GMT 2018] Executing as [email protected] on Linux 4.4.0-43-Microsoft amd64; OpenJDK 64-Bit Server VM 1.8.0_151-8u151-b12-0ubuntu0.16.04.2-b12; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.0.4.0
INFO 2018-05-06 17:11:16 LiftoverVcf Loading up the target reference genome.
[Sun May 06 17:11:16 GMT 2018] picard.vcf.LiftoverVcf done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=503840768
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
java.lang.NullPointerException
at picard.vcf.LiftoverVcf.doWork(LiftoverVcf.java:271)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:282)
at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:25)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)

VCF Header

fileformat=VCFv4.1

ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">

FILTER=<ID=LowQual,Description="Low quality">

FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">

FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">

FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">

FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">

FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">

FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">

FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">

FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">

FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">

GATKCommandLine=<ID=GenotypeGVCFs,Version=3.3-0-g37228af,Date="Sun Apr 08 06:35:15 UTC 2018",Epoch=1523169315240,CommandLineOptions="analysis_type=GenotypeGVCFs input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/l3bioinfo/hg19.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false variant=[(RodBindingCollection [(RodBinding name=variant source=chr1.markdup.recal.g.vcf.gz)])] out=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub includeNonVariantSites=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=10.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=2 annotation=[InbreedingCoeff, FisherStrand, QualByDepth, ChromosomeCounts, GenotypeSummaries, StrandOddsRatio] dbsnp=(RodBinding name= source=UNBOUND) filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">

GATKCommandLine=<ID=SelectVariants,Version=3.3-0-g37228af,Date="Sun Apr 08 06:58:11 UTC 2018",Epoch=1523170691975,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/l3bioinfo/hg19.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/l3bioinfo/55001705017931A.vcf.gz) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] select_expressions=[] excludeNonVariants=true excludeFiltered=false restrictAllelesTo=ALL keepOriginalAC=false mendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[SNP] keepIDs=null fullyDecode=false forceGenotypesDecode=false justRead=false maxIndelSize=2147483647 ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">

GVCFBlock=minGQ=0(inclusive),maxGQ=1(exclusive)

INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">

INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">

INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">

INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">

INFO=<ID=CCC,Number=1,Type=Integer,Description="Number of called chromosomes">

INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">

INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">

INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">

INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">

INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">

INFO=<ID=GQ_MEAN,Number=1,Type=Float,Description="Mean of all GQ values">

INFO=<ID=GQ_STDDEV,Number=1,Type=Float,Description="Standard deviation of all GQ values">

INFO=<ID=HWP,Number=1,Type=Float,Description="P value from test of Hardy Weinberg Equilibrium">

INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">

INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">

INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">

INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">

INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">

INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">

INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">

INFO=<ID=NCC,Number=1,Type=Integer,Description="Number of no-called samples">

INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">

INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">

INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">

contig=<ID=chrM,length=16571,assembly=hg19>

contig=<ID=chr1,length=249250621,assembly=hg19>

contig=<ID=chr2,length=243199373,assembly=hg19>

contig=<ID=chr3,length=198022430,assembly=hg19>

contig=<ID=chr4,length=191154276,assembly=hg19>

contig=<ID=chr5,length=180915260,assembly=hg19>

contig=<ID=chr6,length=171115067,assembly=hg19>

contig=<ID=chr7,length=159138663,assembly=hg19>

contig=<ID=chr8,length=146364022,assembly=hg19>

contig=<ID=chr9,length=141213431,assembly=hg19>

contig=<ID=chr10,length=135534747,assembly=hg19>

contig=<ID=chr11,length=135006516,assembly=hg19>

contig=<ID=chr12,length=133851895,assembly=hg19>

contig=<ID=chr13,length=115169878,assembly=hg19>

contig=<ID=chr14,length=107349540,assembly=hg19>

contig=<ID=chr15,length=102531392,assembly=hg19>

contig=<ID=chr16,length=90354753,assembly=hg19>

contig=<ID=chr17,length=81195210,assembly=hg19>

contig=<ID=chr18,length=78077248,assembly=hg19>

contig=<ID=chr19,length=59128983,assembly=hg19>

contig=<ID=chr20,length=63025520,assembly=hg19>

contig=<ID=chr21,length=48129895,assembly=hg19>

contig=<ID=chr22,length=51304566,assembly=hg19>

contig=<ID=chrX,length=155270560,assembly=hg19>

contig=<ID=chrY,length=59373566,assembly=hg19>

contig=<ID=chr1_gl000191_random,length=106433,assembly=hg19>

contig=<ID=chr1_gl000192_random,length=547496,assembly=hg19>

contig=<ID=chr4_ctg9_hap1,length=590426,assembly=hg19>

contig=<ID=chr4_gl000193_random,length=189789,assembly=hg19>

contig=<ID=chr4_gl000194_random,length=191469,assembly=hg19>

contig=<ID=chr6_apd_hap1,length=4622290,assembly=hg19>

contig=<ID=chr6_cox_hap2,length=4795371,assembly=hg19>

contig=<ID=chr6_dbb_hap3,length=4610396,assembly=hg19>

contig=<ID=chr6_mann_hap4,length=4683263,assembly=hg19>

contig=<ID=chr6_mcf_hap5,length=4833398,assembly=hg19>

contig=<ID=chr6_qbl_hap6,length=4611984,assembly=hg19>

contig=<ID=chr6_ssto_hap7,length=4928567,assembly=hg19>

contig=<ID=chr7_gl000195_random,length=182896,assembly=hg19>

contig=<ID=chr8_gl000196_random,length=38914,assembly=hg19>

contig=<ID=chr8_gl000197_random,length=37175,assembly=hg19>

contig=<ID=chr9_gl000198_random,length=90085,assembly=hg19>

contig=<ID=chr9_gl000199_random,length=169874,assembly=hg19>

contig=<ID=chr9_gl000200_random,length=187035,assembly=hg19>

contig=<ID=chr9_gl000201_random,length=36148,assembly=hg19>

contig=<ID=chr11_gl000202_random,length=40103,assembly=hg19>

contig=<ID=chr17_ctg5_hap1,length=1680828,assembly=hg19>

contig=<ID=chr17_gl000203_random,length=37498,assembly=hg19>

contig=<ID=chr17_gl000204_random,length=81310,assembly=hg19>

contig=<ID=chr17_gl000205_random,length=174588,assembly=hg19>

contig=<ID=chr17_gl000206_random,length=41001,assembly=hg19>

contig=<ID=chr18_gl000207_random,length=4262,assembly=hg19>

contig=<ID=chr19_gl000208_random,length=92689,assembly=hg19>

contig=<ID=chr19_gl000209_random,length=159169,assembly=hg19>

contig=<ID=chr21_gl000210_random,length=27682,assembly=hg19>

contig=<ID=chrUn_gl000211,length=166566,assembly=hg19>

contig=<ID=chrUn_gl000212,length=186858,assembly=hg19>

contig=<ID=chrUn_gl000213,length=164239,assembly=hg19>

contig=<ID=chrUn_gl000214,length=137718,assembly=hg19>

contig=<ID=chrUn_gl000215,length=172545,assembly=hg19>

contig=<ID=chrUn_gl000216,length=172294,assembly=hg19>

contig=<ID=chrUn_gl000217,length=172149,assembly=hg19>

contig=<ID=chrUn_gl000218,length=161147,assembly=hg19>

contig=<ID=chrUn_gl000219,length=179198,assembly=hg19>

contig=<ID=chrUn_gl000220,length=161802,assembly=hg19>

contig=<ID=chrUn_gl000221,length=155397,assembly=hg19>

contig=<ID=chrUn_gl000222,length=186861,assembly=hg19>

contig=<ID=chrUn_gl000223,length=180455,assembly=hg19>

contig=<ID=chrUn_gl000224,length=179693,assembly=hg19>

contig=<ID=chrUn_gl000225,length=211173,assembly=hg19>

contig=<ID=chrUn_gl000226,length=15008,assembly=hg19>

contig=<ID=chrUn_gl000227,length=128374,assembly=hg19>

contig=<ID=chrUn_gl000228,length=129120,assembly=hg19>

contig=<ID=chrUn_gl000229,length=19913,assembly=hg19>

contig=<ID=chrUn_gl000230,length=43691,assembly=hg19>

contig=<ID=chrUn_gl000231,length=27386,assembly=hg19>

contig=<ID=chrUn_gl000232,length=40652,assembly=hg19>

contig=<ID=chrUn_gl000233,length=45941,assembly=hg19>

contig=<ID=chrUn_gl000234,length=40531,assembly=hg19>

contig=<ID=chrUn_gl000235,length=34474,assembly=hg19>

contig=<ID=chrUn_gl000236,length=41934,assembly=hg19>

contig=<ID=chrUn_gl000237,length=45867,assembly=hg19>

contig=<ID=chrUn_gl000238,length=39939,assembly=hg19>

contig=<ID=chrUn_gl000239,length=33824,assembly=hg19>

contig=<ID=chrUn_gl000240,length=41933,assembly=hg19>

contig=<ID=chrUn_gl000241,length=42152,assembly=hg19>

contig=<ID=chrUn_gl000242,length=43523,assembly=hg19>

contig=<ID=chrUn_gl000243,length=43341,assembly=hg19>

contig=<ID=chrUn_gl000244,length=39929,assembly=hg19>

contig=<ID=chrUn_gl000245,length=36651,assembly=hg19>

contig=<ID=chrUn_gl000246,length=38154,assembly=hg19>

contig=<ID=chrUn_gl000247,length=36422,assembly=hg19>

contig=<ID=chrUn_gl000248,length=39786,assembly=hg19>

contig=<ID=chrUn_gl000249,length=38502,assembly=hg19>

Sample SNP From VCF
chr1 864726 . T A 1534.77 . AC=2;AF=1.00;AN=2;DP=41;FS=0.000;GQ_MEAN=120.00;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;NCC=0;QD=29.83;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,40:40:99:1563,120,0
chr1 864755 . A G 2082.77 . AC=2;AF=1.00;AN=2;DP=47;FS=0.000;GQ_MEAN=144.00;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;NCC=0;QD=33.94;SOR=1.378 GT:AD:DP:GQ:PGT:PID:PL 1/1:0,47:47:99:1|1:864755_A_G:2111,144,0

Tagged:

Best Answer

Answers

  • SheilaSheila Broad InstituteMember, Broadie admin

    @dbm
    Hi,

    I don't see anything wrong with your command. Can you try using the Picard standalone version? Let us know if that works. If it does, it may be a version issue with the one in GATK.

    Thanks,
    Sheila

  • dbmdbm Member

    Thank-you @Sheila

    Please see below. i am using this picard version
    https://github.com/broadinstitute/picard/releases/download/2.18.4/picard.jar

    [email protected]:/mnt/e/Various/Genome# java -jar picard.jar LiftoverVcf \

    I=55001705017931A.raw.snp.vcf \
    O=55001705017931A_hg38.raw.snp.vcf \
    CHAIN=hg19ToHg38.over.chain \
    R=hg38.fa \
    REJECT=55001705017931A_hg38_reject.raw.snp.vcf

    21:30:25.157 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/mnt/e/Various/Genome/picard.jar!/com/intel/gkl/native/libgkl_compression.so
    [Wed May 09 21:30:25 GMT 2018] LiftoverVcf INPUT=55001705017931A.raw.snp.vcf OUTPUT=55001705017931A_hg38.raw.snp.vcf CHAIN=hg19ToHg38.over.chain REJECT=55001705017931A_hg38_reject.raw.snp.vcf REFERENCE_SEQUENCE=hg38.fa 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 May 09 21:30:25 GMT 2018] Executing as [email protected] on Linux 4.4.0-43-Microsoft amd64; OpenJDK 64-Bit Server VM 1.8.0_151-8u151-b12-0ubuntu0.16.04.2-b12; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.4-SNAPSHOT
    INFO 2018-05-09 21:30:25 LiftoverVcf Loading up the target reference genome.
    [Wed May 09 21:30:25 GMT 2018] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes.
    Runtime.totalMemory()=514850816
    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]:/mnt/e/Various/Genome#

  • JieChengJieCheng Member

    Hi ,
    @Sheila
    I met the same question with him . And I can make sure that the .dict file and/or .fai file was not missing for the reference. Could you please give me some help? Thanks.

    These are my codes.
    time ~/gatk-4.0.11.0/gatk SelectVariants -R ~/reference/hg19.fa -V ~/MT-1/outname_filtered.snp.vcf -select-type INDEL -O ~/MT-1/outname_raw.snp.indels.vcf
    time ~/gatk-4.0.11.0/gatk VariantFiltration -R ~/reference/hg19.fa -V ~/MT-1/outname_raw.snp.indels.vcf --filter-expression "QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0" --filter-name "my_snp_indel_filter" -O ~/MT-1/outname_filtered.snp.indel.vcf

    And these are the results of outname_filtered.snp.indel.vcf.

    fileformat=VCFv4.2

    ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">

    FILTER=<ID=LowQual,Description="Low quality">

    FILTER=<ID=my_snp_filter,Description="QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0">

    FILTER=<ID=my_snp_indel_filter,Description="QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0">

    FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">

    FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">

    FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">

    FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">

    FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">

    FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">

    FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">

    FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">

    FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">

    FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">

    GATKCommandLine=<ID=CombineGVCFs,CommandLine="CombineGVCFs --output /home/chenjie1/MT-1/outname.HC.g.vc.gz --variant /home/chenjie1/MT-1/sample.HC.g.vcf.gz --reference /home/chenjie1/reference/hg19.fa --convert-to-base-pair-resolution false --break-bands-at-multiples-of 0 --ignore-variants-starting-outside-interval false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --disable-tool-default-annotations false --enable-all-annotations false",Version=4.0.11.0,Date="November 3, 2018 8:08:35 PM CST">

    GATKCommandLine=<ID=SelectVariants,CommandLine="SelectVariants --output outname_raw.snp.indels.vcf --select-type-to-include INDEL --variant /home/chenjie1/MT-1/outname_filtered.snp.vcf --reference /home/chenjie1/reference/hg19.fa --invertSelect false --exclude-non-variants false --exclude-filtered false --preserve-alleles false --remove-unused-alternates false --restrict-alleles-to ALL --keep-original-ac false --keep-original-dp false --mendelian-violation false --invert-mendelian-violation false --mendelian-violation-qual-threshold 0.0 --select-random-fraction 0.0 --remove-fraction-genotypes 0.0 --fully-decode false --max-indel-size 2147483647 --min-indel-size 0 --max-filtered-genotypes 2147483647 --min-filtered-genotypes 0 --max-fraction-filtered-genotypes 1.0 --min-fraction-filtered-genotypes 0.0 --max-nocall-number 2147483647 --max-nocall-fraction 1.0 --set-filtered-gt-to-nocall false --allow-nonoverlapping-command-line-samples false --suppress-reference-path false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",Version=4.0.11.0,Date="November 9, 2018 3:52:22 PM CST">

    GATKCommandLine=<ID=VariantFiltration,CommandLine="VariantFiltration --output /home/chenjie1/MT-1/outname_filtered.snp.indel.vcf --filter-expression QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0 --filter-name my_snp_indel_filter --variant /home/chenjie1/MT-1/outname_raw.snp.indels.vcf --reference /home/chenjie1/reference/hg19.fa --cluster-size 3 --cluster-window-size 0 --mask-extension 0 --mask-name Mask --filter-not-in-mask false --missing-values-evaluate-as-failing false --invalidate-previous-filters false --invert-filter-expression false --invert-genotype-filter-expression false --set-filtered-genotype-to-no-call false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",Version=4.0.11.0,Date="November 9, 2018 4:00:54 PM CST">

    INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">

    INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">

    INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">

    INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">

    INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">

    INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">

    INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">

    INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">

    INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">

    INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">

    INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">

    INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">

    INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">

    INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">

    INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">

    INFO=<ID=RAW_MQandDP,Number=2,Type=Integer,Description="Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation.">

    INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">

    INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">

    contig=<ID=chrM,length=16571,assembly=hg19.fa>

    contig=<ID=chr1,length=249250621,assembly=hg19.fa>

    contig=<ID=chr2,length=243199373,assembly=hg19.fa>

    contig=<ID=chr3,length=198022430,assembly=hg19.fa>

    contig=<ID=chr4,length=191154276,assembly=hg19.fa>

    contig=<ID=chr5,length=180915260,assembly=hg19.fa>

    contig=<ID=chr6,length=171115067,assembly=hg19.fa>

    contig=<ID=chr7,length=159138663,assembly=hg19.fa>

    contig=<ID=chr8,length=146364022,assembly=hg19.fa>

    contig=<ID=chr9,length=141213431,assembly=hg19.fa>

    contig=<ID=chr10,length=135534747,assembly=hg19.fa>

    contig=<ID=chr11,length=135006516,assembly=hg19.fa>

    contig=<ID=chr12,length=133851895,assembly=hg19.fa>

    contig=<ID=chr13,length=115169878,assembly=hg19.fa>

    contig=<ID=chr14,length=107349540,assembly=hg19.fa>

    contig=<ID=chr15,length=102531392,assembly=hg19.fa>

    contig=<ID=chr16,length=90354753,assembly=hg19.fa>

    contig=<ID=chr17,length=81195210,assembly=hg19.fa>

    contig=<ID=chr18,length=78077248,assembly=hg19.fa>

    contig=<ID=chr19,length=59128983,assembly=hg19.fa>

    contig=<ID=chr20,length=63025520,assembly=hg19.fa>

    contig=<ID=chr21,length=48129895,assembly=hg19.fa>

    contig=<ID=chr22,length=51304566,assembly=hg19.fa>

    contig=<ID=chrX,length=155270560,assembly=hg19.fa>

    contig=<ID=chrY,length=59373566,assembly=hg19.fa>

    contig=<ID=chr1_gl000191_random,length=106433,assembly=hg19.fa>

    contig=<ID=chr1_gl000192_random,length=547496,assembly=hg19.fa>

    contig=<ID=chr4_ctg9_hap1,length=590426,assembly=hg19.fa>

    contig=<ID=chr4_gl000193_random,length=189789,assembly=hg19.fa>

    contig=<ID=chr4_gl000194_random,length=191469,assembly=hg19.fa>

    contig=<ID=chr6_apd_hap1,length=4622290,assembly=hg19.fa>

    contig=<ID=chr6_cox_hap2,length=4795371,assembly=hg19.fa>

    contig=<ID=chr6_dbb_hap3,length=4610396,assembly=hg19.fa>

    contig=<ID=chr6_mann_hap4,length=4683263,assembly=hg19.fa>

    contig=<ID=chr6_mcf_hap5,length=4833398,assembly=hg19.fa>

    contig=<ID=chr6_qbl_hap6,length=4611984,assembly=hg19.fa>

    contig=<ID=chr6_ssto_hap7,length=4928567,assembly=hg19.fa>

    contig=<ID=chr7_gl000195_random,length=182896,assembly=hg19.fa>

    contig=<ID=chr8_gl000196_random,length=38914,assembly=hg19.fa>

    contig=<ID=chr8_gl000197_random,length=37175,assembly=hg19.fa>

    contig=<ID=chr9_gl000198_random,length=90085,assembly=hg19.fa>

    contig=<ID=chr9_gl000199_random,length=169874,assembly=hg19.fa>

    contig=<ID=chr9_gl000200_random,length=187035,assembly=hg19.fa>

    contig=<ID=chr9_gl000201_random,length=36148,assembly=hg19.fa>

    contig=<ID=chr11_gl000202_random,length=40103,assembly=hg19.fa>

    contig=<ID=chr17_ctg5_hap1,length=1680828,assembly=hg19.fa>

    contig=<ID=chr17_gl000203_random,length=37498,assembly=hg19.fa>

    contig=<ID=chr17_gl000204_random,length=81310,assembly=hg19.fa>

    contig=<ID=chr17_gl000205_random,length=174588,assembly=hg19.fa>

    contig=<ID=chr17_gl000206_random,length=41001,assembly=hg19.fa>

    contig=<ID=chr18_gl000207_random,length=4262,assembly=hg19.fa>

    contig=<ID=chr19_gl000208_random,length=92689,assembly=hg19.fa>

    contig=<ID=chr19_gl000209_random,length=159169,assembly=hg19.fa>

    contig=<ID=chr21_gl000210_random,length=27682,assembly=hg19.fa>

    contig=<ID=chrUn_gl000211,length=166566,assembly=hg19.fa>

    contig=<ID=chrUn_gl000212,length=186858,assembly=hg19.fa>

    contig=<ID=chrUn_gl000213,length=164239,assembly=hg19.fa>

    contig=<ID=chrUn_gl000214,length=137718,assembly=hg19.fa>

    contig=<ID=chrUn_gl000215,length=172545,assembly=hg19.fa>

    contig=<ID=chrUn_gl000216,length=172294,assembly=hg19.fa>

    contig=<ID=chrUn_gl000217,length=172149,assembly=hg19.fa>

    contig=<ID=chrUn_gl000218,length=161147,assembly=hg19.fa>

    contig=<ID=chrUn_gl000219,length=179198,assembly=hg19.fa>

    contig=<ID=chrUn_gl000220,length=161802,assembly=hg19.fa>

    contig=<ID=chrUn_gl000221,length=155397,assembly=hg19.fa>

    contig=<ID=chrUn_gl000222,length=186861,assembly=hg19.fa>

    contig=<ID=chrUn_gl000223,length=180455,assembly=hg19.fa>

    contig=<ID=chrUn_gl000224,length=179693,assembly=hg19.fa>

    contig=<ID=chrUn_gl000225,length=211173,assembly=hg19.fa>

    contig=<ID=chrUn_gl000226,length=15008,assembly=hg19.fa>

    contig=<ID=chrUn_gl000227,length=128374,assembly=hg19.fa>

    contig=<ID=chrUn_gl000228,length=129120,assembly=hg19.fa>

    contig=<ID=chrUn_gl000229,length=19913,assembly=hg19.fa>

    contig=<ID=chrUn_gl000230,length=43691,assembly=hg19.fa>

    contig=<ID=chrUn_gl000231,length=27386,assembly=hg19.fa>

    contig=<ID=chrUn_gl000232,length=40652,assembly=hg19.fa>

    contig=<ID=chrUn_gl000233,length=45941,assembly=hg19.fa>

    contig=<ID=chrUn_gl000234,length=40531,assembly=hg19.fa>

    contig=<ID=chrUn_gl000235,length=34474,assembly=hg19.fa>

    contig=<ID=chrUn_gl000236,length=41934,assembly=hg19.fa>

    contig=<ID=chrUn_gl000237,length=45867,assembly=hg19.fa>

    contig=<ID=chrUn_gl000238,length=39939,assembly=hg19.fa>

    contig=<ID=chrUn_gl000239,length=33824,assembly=hg19.fa>

    contig=<ID=chrUn_gl000240,length=41933,assembly=hg19.fa>

    contig=<ID=chrUn_gl000241,length=42152,assembly=hg19.fa>

    contig=<ID=chrUn_gl000242,length=43523,assembly=hg19.fa>

    contig=<ID=chrUn_gl000243,length=43341,assembly=hg19.fa>

    contig=<ID=chrUn_gl000244,length=39929,assembly=hg19.fa>

    contig=<ID=chrUn_gl000245,length=36651,assembly=hg19.fa>

    contig=<ID=chrUn_gl000246,length=38154,assembly=hg19.fa>

    contig=<ID=chrUn_gl000247,length=36422,assembly=hg19.fa>

    contig=<ID=chrUn_gl000248,length=39786,assembly=hg19.fa>

    contig=<ID=chrUn_gl000249,length=38502,assembly=hg19.fa>

    reference=file:///home/chenjie1/reference/hg19.fa

    source=CombineGVCFs

    source=SelectVariants

    source=VariantFiltration

    CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample_name

    Best regards.
    Jie

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @JieCheng

    Whats the error here? Please post the entire error log.

    Regards
    Bhanu

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