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Query regarding picard liftoverVcf

tanu06tanu06 CanadaMember
edited October 2018 in Ask the GATK team

have been running liftoverVcf between genomes of the honey bee, it is successfully running but none of the SNPs are getting lifted over.
Command :

java -jar picard.jar LiftoverVcf I=/data2/OUTPUT/snp/5074_snp_R3_final.vcf.gz O=5074_lifted_over.vcf CHAIN=amel4.5toHAV3.1.over.chain.gz REJECT=5074_rejected_variants.vcf R=HAv3.1_genome.fa WARN_ON_MISSING_CONTIG=true
Output
 java -jar picard.jar LiftoverVcf I=1007_snp_R3_final.vcf O=1024_lifted_over.vcf CHAIN=amel4.5toHAV3.1.over.chain.gz REJECT=1024_rejected_variants.vcf R=HAv3.1_genome.fa
INFO    2018-10-12 11:37:01     LiftoverVcf

********** 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:
**********
**********    LiftoverVcf -I 1007_snp_R3_final.vcf -O 1024_lifted_over.vcf -CHAIN amel4.5toHAV3.1.over.chain.gz -REJECT 1024_rejected_variants.vcf -R HAv3.1_genome.fa
**********


11:37:01.545 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/data2/side_analysis/picard_liftover/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Fri Oct 12 11:37:01 EDT 2018] LiftoverVcf INPUT=1007_snp_R3_final.vcf OUTPUT=1024_lifted_over.vcf CHAIN=amel4.5toHAV3.1.over.chain.gz REJECT=1024_rejected_variants.vcf REFERENCE_SEQUENCE=HAv3.1_genome.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
[Fri Oct 12 11:37:01 EDT 2018] Executing as [email protected] on Linux 4.4.0-124-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_121-b13; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.14-SNAPSHOT
INFO    2018-10-12 11:37:02     LiftoverVcf     Loading up the target reference genome.
INFO    2018-10-12 11:37:03     LiftoverVcf     Lifting variants over and sorting (not yet writing the output file.)
INFO    2018-10-12 11:37:18     LiftoverVcf     Processed 1654903 variants.
INFO    2018-10-12 11:37:18     LiftoverVcf     1654903 variants failed to liftover.
INFO    2018-10-12 11:37:18     LiftoverVcf     0 variants lifted over but had mismatching reference alleles after lift over.
INFO    2018-10-12 11:37:18     LiftoverVcf     100.0000% of variants were not successfully lifted over and written to the output.
INFO    2018-10-12 11:37:18     LiftoverVcf     liftover success by source contig:
INFO    2018-10-12 11:37:18     LiftoverVcf     1.1: 0 / 11968 (0.0000%)
INFO    2018-10-12 11:37:18     LiftoverVcf     1.10: 0 / 11140 (0.0000%)
INFO    2018-10-12 11:37:18     LiftoverVcf     1.11: 0 / 5 (0.0000%)
INFO    2018-10-12 11:37:18     LiftoverVcf     1.12: 0 / 5 (0.0000%)
INFO    2018-10-12 11:37:18     LiftoverVcf     1.13: 0 / 6 (0.0000%)
INFO    2018-10-12 11:37:18     LiftoverVcf     1.14: 0 / 2781 (0.0000%)
INFO    2018-10-12 11:37:18     LiftoverVcf     1.15: 0 / 10992 (0.0000%)
INFO    2018-10-12 12:14:10     LiftoverVcf     lifted variants by target contig:
INFO    2018-10-12 12:14:10     LiftoverVcf     no successfully lifted variants
WARNING 2018-10-12 12:14:10     LiftoverVcf     0 variants with a swapped REF/ALT were identified, but were not recovered.  See RECOVER_SWAPPED_REF_ALT and associated caveats.
INFO    2018-10-12 12:14:10     LiftoverVcf     Writing out sorted records to final VCF.
[Fri Oct 12 12:14:10 EDT 2018] picard.vcf.LiftoverVcf done. Elapsed time: 0.20 minutes.
Runtime.totalMemory()=3609722880

It is making the output files too.

Any suggestions or link which can help me.
Thank You,
With Regards,
Tanushree

Post edited by shlee on

Best Answers

Answers

  • yfarjounyfarjoun Broad InstituteDev ✭✭✭

    Tanushree,

    Could you please post a few lines of the reject VCF?

  • tanu06tanu06 CanadaMember
    edited October 2018

    sure. Thank you for your prompt reply.

    ##fileformat=VCFv4.2
    ##FILTER=<ID=IndelStraddlesMultipleIntevals,Description="Reference allele in Indel is straddling multiple intervals in the chain, and so the results are not well defined.">
    ##FILTER=<ID=MismatchedRefAllele,Description="Reference allele does not match reference genome sequence after liftover.">
    ##FILTER=<ID=NoTarget,Description="Variant could not be lifted between genome builds.">
    ##FILTER=<ID=ReverseComplementedIndel,Description="Indel falls into a reverse complemented region in the target genome.">
    ##FILTER=<ID=indel,Description="Overlaps a user-input mask">
    ##FILTER=<ID=min_dp_10,Description="Minimum Coverage 10">
    ##FILTER=<ID=min_indelqual_67,Description="Minimum Indel Quality (Phred) 67">
    ##FILTER=<ID=min_indelqual_88,Description="Minimum Indel Quality (Phred) 88">
    ##FILTER=<ID=min_snvqual_101,Description="Minimum SNV Quality (Phred) 101">
    ##FILTER=<ID=min_snvqual_80,Description="Minimum SNV Quality (Phred) 80">
    ##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
    ##GATKCommandLine.VariantFiltration=<ID=VariantFiltration,CommandLineOptions="analysis_type=VariantFiltration input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filte
    r=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data2/training_set/AM45/am45new.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 max
    RuntimeUnits=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_qual
    ity_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscore
    s_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_cmdl
    ine_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 monito
    rThreadEfficiency=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 var
    iant_index_parameter=-1 reference_window_stop=0 logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=5074_snp.vcf) mask=(RodBinding name=mask source=/data2/training_set/Training_set/INDEL_T
    RAINING.vcf) out=/data3/Run31.1/5074_snp_R1.vcf filterExpression=[] filterName=[] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskExtension=5 maskName=indel filterNotInMask=false missingValuesInExp
    ressionsShouldEvaluateAsFailing=false invalidatePreviousFilters=false invertFilterExpression=false invertGenotypeFilterExpression=false setFilteredGtToNocall=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false f
    ilter_bases_not_stored=false",Date="Fri Jul 28 10:08:12 EDT 2017",Epoch=1501250892404,Version=3.5-0-g36282e4>
    ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
    ##INFO=<ID=AttemptedLocus,Number=1,Type=String,Description="The locus of the variant in the TARGET prior to failing due to mismatching alleles.">
    ##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
    ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
    ##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
    ##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
    ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
    ##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
    ##contig=<ID=1.1,length=1382403>
    ##contig=<ID=1.2,length=890726>
    ##contig=<ID=1.3,length=797889>
    ##contig=<ID=1.4,length=319845>
    ##contig=<ID=1.5,length=606820>
    ##contig=<ID=1.6,length=188607>
    ##contig=<ID=1.7,length=704741>
    ##contig=<ID=1.8,length=367308>
    ##contig=<ID=1.9,length=219847>
    ##contig=<ID=1.10,length=1405242>
    ##contig=<ID=1.11,length=2557>
    ##contig=<ID=1.12,length=4728>
    ##contig=<ID=1.13,length=5741>
    ##contig=<ID=1.14,length=451513>
    ##contig=<ID=1.15,length=1227296>
    ##contig=<ID=1.16,length=731410>
    ##contig=<ID=1.17,length=716596>
    ##contig=<ID=1.18,length=166954>
    ##contig=<ID=1.19,length=370959>
    ##contig=<ID=1.20,length=48872>
    ##contig=<ID=1.21,length=673331>
    ##contig=<ID=1.22,length=682149>
    ##contig=<ID=1.23,length=1527290>
    ##contig=<ID=1.24,length=1962>
    ##contig=<ID=1.25,length=449272>
    ##contig=<ID=1.26,length=90960>
    ##contig=<ID=1.27,length=417775>
    ##contig=<ID=1.28,length=158922>
    ##contig=<ID=1.29,length=1952552>
    ##contig=<ID=1.30,length=232100>
    ##contig=<ID=1.31,length=758083>
    .
    .
    .
    ##contig=<ID=17.5307,length=909>
    ##contig=<ID=17.5308,length=865>
    ##fileDate=20170728
    ##reference=file:///data2/training_set/AM45/am45new.fasta
    ##source=lofreq call --call-indels -f /data2/training_set/AM45/am45new.fasta --no-default-filter -r 1.1:1-1382403 -o /tmp/lofreq2_call_parallelvAhn7b/0.vcf.gz 5074_BQSR.bam
    #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
    1.1     1348    .       C       T       1795    NoTarget        AF=0.666667;DP=171;DP4=21,36,57,57;SB=8
    1.1     1493    .       T       G       175     NoTarget        AF=0.177570;DP=107;DP4=38,47,3,17;SB=16
    1.1     1523    .       A       T       1827    NoTarget        AF=0.955056;DP=89;DP4=1,3,35,50;SB=1
    1.1     1834    .       T       C       542     NoTarget        AF=0.363636;DP=99;DP4=28,35,20,16;SB=5
    1.1     1920    .       G       A       160     NoTarget        AF=0.169492;DP=118;DP4=50,48,13,7;SB=4
    1.1     1933    .       T       C       218     NoTarget        AF=0.198347;DP=121;DP4=52,45,14,10;SB=0.
    

    This is my vcf file entries which I want to get lifted to the new genome.

    With regards,
    Tanushree

    Post edited by shlee on
  • yfarjounyfarjoun Broad InstituteDev ✭✭✭

    right, but I asked for the REJECT_VCF that was created by the LiftoverVcf tool....that is 1024_rejected_variants.vcf

  • tanu06tanu06 CanadaMember
    edited October 2018

    yes, it is xxxx_rejected_variants.vcf

    ##fileformat=VCFv4.2
    ##FILTER=<ID=IndelStraddlesMultipleIntevals,Description="Reference allele in Indel is straddling multiple intervals in the chain, and so the results are not well defined.">
    ##FILTER=<ID=MismatchedRefAllele,Description="Reference allele does not match reference genome sequence after liftover.">
    ##FILTER=<ID=NoTarget,Description="Variant could not be lifted between genome builds.">
    ##FILTER=<ID=ReverseComplementedIndel,Description="Indel falls into a reverse complemented region in the target genome.">
    ##FILTER=<ID=indel,Description="Overlaps a user-input mask">
    ##FILTER=<ID=min_dp_10,Description="Minimum Coverage 10">
    ##FILTER=<ID=min_indelqual_67,Description="Minimum Indel Quality (Phred) 67">
    ##FILTER=<ID=min_indelqual_88,Description="Minimum Indel Quality (Phred) 88">
    ##FILTER=<ID=min_snvqual_101,Description="Minimum SNV Quality (Phred) 101">
    ##FILTER=<ID=min_snvqual_80,Description="Minimum SNV Quality (Phred) 80">
    ##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
    ##GATKCommandLine.VariantFiltration=<ID=VariantFiltration,CommandLineOptions="analysis_type=VariantFiltration input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data2/training_set/AM45/am45new.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 static_quantized_quals=null round_down_quantized=false 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 reference_window_stop=0 logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=5074_snp.vcf) mask=(RodBinding name=mask source=/data2/training_set/Training_set/INDEL_TRAINING.vcf) out=/data3/Run31.1/5074_snp_R1.vcf filterExpression=[] filterName=[] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskExtension=5 maskName=indel filterNotInMask=false missingValuesInExpressionsShouldEvaluateAsFailing=false invalidatePreviousFilters=false invertFilterExpression=false invertGenotypeFilterExpression=false setFilteredGtToNocall=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Fri Jul 28 10:08:12 EDT 2017",Epoch=1501250892404,Version=3.5-0-g36282e4>
    ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
    ##INFO=<ID=AttemptedLocus,Number=1,Type=String,Description="The locus of the variant in the TARGET prior to failing due to mismatching alleles.">
    ##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
    ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
    ##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
    ##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
    ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
    ##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
    ##contig=<ID=1.1,length=1382403>
    ##contig=<ID=1.2,length=890726>
    ##contig=<ID=1.3,length=797889>
    ##contig=<ID=1.4,length=319845>
    ##contig=<ID=1.5,length=606820>
    ##contig=<ID=1.6,length=188607>
    ##contig=<ID=1.7,length=704741>
    ##contig=<ID=1.8,length=367308>
    ##contig=<ID=1.9,length=219847>
    ##contig=<ID=1.10,length=1405242>
    ##contig=<ID=1.11,length=2557>
    ##contig=<ID=1.12,length=4728>
    ##contig=<ID=1.13,length=5741>
    ##contig=<ID=1.14,length=451513>
    ##contig=<ID=1.15,length=1227296>
    ##contig=<ID=1.16,length=731410>
    ##contig=<ID=1.17,length=716596>
    ##contig=<ID=1.18,length=166954>
    ##contig=<ID=1.19,length=370959>
    ##contig=<ID=1.20,length=48872>
    ##contig=<ID=1.21,length=673331>
    ##contig=<ID=1.22,length=682149>
    ##contig=<ID=1.23,length=1527290>
    ##contig=<ID=1.24,length=1962>
    ##contig=<ID=1.25,length=449272>
    ##contig=<ID=1.26,length=90960>
    ##contig=<ID=1.27,length=417775>
    ##contig=<ID=1.28,length=158922>
    ##contig=<ID=1.29,length=1952552>
    ##contig=<ID=1.30,length=232100>
    ##contig=<ID=1.31,length=758083>
    .
    .
    .
    ##contig=<ID=17.5302,length=981>
    ##contig=<ID=17.5303,length=960>
    ##contig=<ID=17.5304,length=959>
    ##contig=<ID=17.5305,length=951>
    ##contig=<ID=17.5306,length=861>
    ##contig=<ID=17.5307,length=909>
    ##contig=<ID=17.5308,length=865>
    ##fileDate=20170728
    ##reference=file:///data2/training_set/AM45/am45new.fasta
    ##source=lofreq call --call-indels -f /data2/training_set/AM45/am45new.fasta --no-default-filter -r 1.1:1-1382403 -o /tmp/lofreq2_call_parallelvAhn7b/0.vcf.gz 5074_BQSR.bam
    #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
    1.1     1348    .       C       T       1795    NoTarget        AF=0.666667;DP=171;DP4=21,36,57,57;SB=8
    1.1     1493    .       T       G       175     NoTarget        AF=0.177570;DP=107;DP4=38,47,3,17;SB=16
    1.1     1523    .       A       T       1827    NoTarget        AF=0.955056;DP=89;DP4=1,3,35,50;SB=1
    1.1     1834    .       T       C       542     NoTarget        AF=0.363636;DP=99;DP4=28,35,20,16;SB=5
    1.1     1920    .       G       A       160     NoTarget        AF=0.169492;DP=118;DP4=50,48,13,7;SB=4
    1.1     1933    .       T       C       218     NoTarget        AF=0.198347;DP=121;DP4=52,45,14,10;SB=0
    1.1     2076    .       G       A       169     NoTarget        AF=0.222222;DP=99;DP4=28,44,9,13;SB=0
    1.1     2083    .       A       G       349     NoTarget        AF=0.288660;DP=97;DP4=25,44,13,15;SB=4
    1.1     2120    .       A       C       363     NoTarget        AF=0.304348;DP=92;DP4=23,40,13,16;SB=3
    1.1     2144    .       A       G       405     NoTarget        AF=0.291262;DP=103;DP4=26,46,17,14;SB=10
    1.1     2222    .       G       A       363     NoTarget        AF=0.272727;DP=110;DP4=45,35,16,14;SB=0
    1.1     2224    .       A       T       368     NoTarget        AF=0.266055;DP=109;DP4=44,36,15,14;SB=0
    1.1     2236    .       C       T       377     NoTarget        AF=0.287129;DP=101;DP4=37,35,17,12;SB=1
    1.1     2347    .       C       T       362     NoTarget        AF=0.339450;DP=109;DP4=35,37,18,19;SB=0
    1.1     2362    .       G       A       950     NoTarget        AF=0.577586;DP=116;DP4=26,23,31,36;SB=2
    1.1     2422    .       G       A       598     NoTarget        AF=0.363636;DP=121;DP4=43,34,22,22;SB=2
    1.1     3015    .       G       A       547     NoTarget        AF=0.261438;DP=153;DP4=50,63,15,25;SB=2
    1.1     3088    .       G       A       819     NoTarget        AF=0.371622;DP=148;DP4=40,52,28,27;SB=4
    1.1     3098    .       G       A       3274    NoTarget        AF=0.986301;DP=146;DP4=0,0,69,75;SB=0
    1.1     4823    .       A       G       701     NoTarget        AF=0.348718;DP=195;DP4=63,64,37,31;SB=2
    1.1     4825    .       G       A       678     NoTarget        AF=0.317949;DP=195;DP4=66,66,33,29;SB=1
    1.1     4827    .       G       A       980     NoTarget        AF=0.392857;DP=196;DP4=57,60,42,35;SB=3
    1.1     4830    .       T       A       4180    NoTarget        AF=0.994845;DP=194;DP4=0,0,100,93;SB=0
    1.1     4853    .       A       T       773     NoTarget        AF=0.329787;DP=188;DP4=66,60,34,28;SB=1
    

    With Regards,
    Tanushree

    Post edited by shlee on
  • yfarjounyfarjoun Broad InstituteDev ✭✭✭

    hmmm. it seems that one of the two references you are providing is wrong, or the chainfile. Otherwise, I do not see how ALL your variants could be failing. please triplecheck your inputs.

  • tanu06tanu06 CanadaMember

    I have tried running by providing both the reference to the program. In my chain file, I used my old genome as query and new genome as a target.
    Any suggestions on it?

    With Regards,
    Tanushree

  • yfarjounyfarjoun Broad InstituteDev ✭✭✭

    can you post the first part of your chain file and the first few records in your reference-dictionary?

  • tanu06tanu06 CanadaMember

    Sure. my chain file looks like this
    chain 209690 QIUM02000100.1 34588 + 3369 8606 17.10 138704 + 43828 48648 2518
    38 1 0
    28 0 1
    23 0 18
    187 2 0
    1297 0 17
    9 1 0
    11 0 1
    9 1 0
    218 2 1
    533 8 0
    309 0 1
    7 0 13
    9 0 1
    17 4 0
    7 2 0
    24 10 0
    25 3 0
    8 0 1
    36 2 0
    10 1 0
    25 1 0
    4 10 0
    16 3 0
    12 9 0
    8 21 0
    10 0 5
    18 7 0
    26 0 4
    10 5 0
    22 0 1
    27 22 0
    8 10 0

    whereas my reference dictionary
    @HD VN:1.5
    @SQ SN:CM009931.2 LN:27754200 M5:9766c763686195c8a21a46adc4956191 UR:file:/data2/side_analysis/picard_liftover/HAv3.1_genome.fa
    @SQ SN:CM009932.2 LN:16089512 M5:10eac95bd7f041788f1ba8807c5f915b UR:file:/data2/side_analysis/picard_liftover/HAv3.1_genome.fa
    @SQ SN:QIUM02000220.1 LN:3988 M5:bd2068e4dc74402b685b589b01537d3b UR:file:/data2/side_analysis/picard_liftover/HAv3.1_genome.fa
    @SQ SN:CM009933.2 LN:13619445 M5:a3a343deb941643c81d994b0a67c642c UR:file:/data2/side_analysis/picard_liftover/HAv3.1_genome.fa
    @SQ SN:CM009934.2 LN:13404451 M5:1f8066dc6d1dedb4bdc2c2d373b2c768 UR:file:/data2/side_analysis/picard_liftover/HAv3.1_genome.fa
    @SQ SN:CM009935.2 LN:13896941 M5:35567cda1aa65c7a957fc9aada823752 UR:file:/data2/side_analysis/picard_liftover/HAv3.1_genome.fa

    With regards,
    Tanushree

  • yfarjounyfarjoun Broad InstituteDev ✭✭✭

    Is that the entire dictionary?

    I ask because I notice that your chain is referencing a sequence (17.10) that isn't in your dictionary...

    this would explain why none of the variants are lifted.

  • tanu06tanu06 CanadaMember

    No it is just few lines of my dictionary file. Is picard lifover is limited to vcf files from Haplotypecaller? As my vcf file is from lofreq.

    With Regards,
    Tanushree

  • tanu06tanu06 CanadaMember

    Secondly, 17.10 is my old genome and the dictionary file I shared is from the new genome which I want 17.10 to be lifterOver.
    QIUM02000100.1 : new genome id
    17.10 : old genome id

    With regards
    Tanushree

  • tanu06tanu06 CanadaMember

    Thank you.
    Reversing my chain file helped. Now i am getting the new vcf file but how do i correlate between the original and lifted over vcf.
    I truly agree the tools should give more helpful error messages.

    With Regards,
    Tanushree

  • tanu06tanu06 CanadaMember

    Thank you, I have my lifted over vcf file with all the required details.
    Thank you for your help and time.

    With Regards,
    Tanushree

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