Readme File for the Atanur_et_al_28Genomes_SNPS_Indels data. This data comes from the paper: http://dx.doi.org/10.1016/j.cell.2013.06.040 PubmedId: PMID: 23890820 The folder contains 3 files 1. 28genome_Indels.vcf.gz 2. 28genome_SNP_part1.vcf.gz 3. 28genome_SNP.part2.vcf.gz The Variants in the files come from 28 rat Strains sequenced across multiple sequencing centers and analysed with the Unified Genotyper. The files are in VCF v4.1 format. 28genome_SNP.part2.vcf.gz does not contain any headers since the 2 SNP files originated as a single large file that was split due to size constraints. After download, these two files should be combined to reconstitute the original file. RGD is working to put this data for visualization and analysis into their Variant Visualizer ( http://rgd.mcw.edu/rgdweb/front/select.html ) and the Rat Genome Browser ( http://rgd.mcw.edu/fgb2/gbrowse/rgd_904/ ). Questions about the data can be sent to the Corresponding author of the paper: t.aitman@csc.mrc.ac.uk Alternatively, questions/concerns can be directed here: http://rgd.mcw.edu/contact/index.shtml Included strains are as follows: Column Headers From Atanur et al (PMID: 23890820) Official Strain Symbol Strain RGD ID Designation in Variant Visualizer ACI ACI/EurMcwi ACI/Eur 1547869 as ACI/Eur sequenced by MCW BBDP BBDP/Wor BBDP/Rhw 10002 BN.Lx BN.Lx BN-Lx 61113 as BN-Lx sequenced by ICL, KNAW EVE ---- BN/NHsdMcwi 61498 Original reference genome strain. F344/Ncrl F344/NCrl F344/NCrl 737926 as F344/N sequenced by KNAW FHH FHH/EurMcwi FHH/EurMcwi 629509 FHH/EurMcwi sequenced by MCW, MDC FHL FHL/EurMcwi FHL/EurMcwi 1581626 FHL/EurMcwi sequenced by MCW GK GK/Ox GK/Ox 4889464 LE/Stm LE/Stm LE/Stm 629485 LE/Stm sequenced by KNAW LEW LEW/Crl LEW/Crl 737932 LEW/NcrlBR LEW/NCrlBR LEW/NCrl 61104 LH LH/MavRrrc LH/MavRrrc 60990 LL LL/MavRrrc LL/MavRrrc 68077 LN LN/MavRrrc LN/MavRrrc 61015 MHS MHS/Gib MHS/Gib 10025 MNS MNS/Gib MNS/Gib 10028 SBH SBH/Ygl SBH/Ygl 631572 SBN SBN/Ygl SBN/Ygl 631573 SHR SHR/OlaIpcv SHR/OlaIpcv 631848 SHR/OlaIpcv sequenced by ICL, KNAW SHR/NHsd SHR/NHsd SHR/NHsd 724574 SHRSP/Gla SHRSP/Gla SHRSP/Gcrc 734759 as SHRSP/Gcrc sequenced by MDC SR/Jr SR/Jr SR/Jr 10040 as SR/JrHsd sequenced by MCW SS/Jr SS/Jr SS/Jr 10041 SS_JRHSDMCWI SS/JrHsdMcwi SS/JrHsdMcwi 61499 as SS/JrHsdMcwi sequenced by MCW, MDC WAG WAG/Rij WAG/Rij 737924 WKY WKY/NCrl WKY/NCrl 1358112 WKY/Gla WKY/Gla WKY/Gcrc 734760 WKY_NHSD WKY/NHsd WKY/NHsd 61105 as WKY/N sequenced by KNAW PLEASE NOTE: the strain EVE in the file corresponds to the rat/strain that was originally sequenced for the reference genome with strain name: BN/NHsdMcwi File headers are reproduced here: 1. 28genome_Indels.vcf.gz ##fileformat=VCFv4.1 ##ApplyRecalibration="analysis_type=ApplyRecalibration input_file=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/tmp/pbs.995595.cx1b/tmp_reference.fa rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null help=false input=[(RodBinding name=input source=/groupvol/pgm/home/satanur/analysis/2012_02_28/indel/28genome/28genome_raw_indel_het06_mmq30_mbq20.vcf)] recal_file=/groupvol/pgm/home/satanur/analysis/2012_02_28/indel/28genome/variant_recal/28genome_raw_indel_8guassian_t30.recal tranches_file=/groupvol/pgm/home/satanur/analysis/2012_02_28/indel/28genome/variant_recal/28genome_raw_indel_8guassian_t30.tranches out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub ts_filter_level=99.0 ignore_filter=null mode=INDEL filter_mismatching_base_and_quals=false" ##CombineVariants="analysis_type=CombineVariants input_file=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/tmp/pbs.992103.cx1b/tmp_reference.fa rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null help=false variant=[(RodBinding name=inputM source=/groupvol/pgm/home/satanur/analysis/2012_02_28/indel/28genome/28genome_raw_indel_het06_mmq30_mbq20_chrM.vcf), (RodBinding name=input1 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/indel/28genome/28genome_raw_indel_het06_mmq30_mbq20_chr1.vcf), (RodBinding name=input2 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/indel/28genome/28genome_raw_indel_het06_mmq30_mbq20_chr2.vcf), (RodBinding name=input3 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/indel/28genome/28genome_raw_indel_het06_mmq30_mbq20_chr3.vcf), (RodBinding name=input4 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/indel/28genome/28genome_raw_indel_het06_mmq30_mbq20_chr4.vcf), (RodBinding name=input5 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/indel/28genome/28genome_raw_indel_het06_mmq30_mbq20_chr5.vcf), (RodBinding name=input6 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/indel/28genome/28genome_raw_indel_het06_mmq30_mbq20_chr6.vcf), (RodBinding name=input7 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/indel/28genome/28genome_raw_indel_het06_mmq30_mbq20_chr7.vcf), (RodBinding name=input8 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/indel/28genome/28genome_raw_indel_het06_mmq30_mbq20_chr8.vcf), (RodBinding name=input9 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/indel/28genome/28genome_raw_indel_het06_mmq30_mbq20_chr9.vcf), (RodBinding name=input10 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/indel/28genome/28genome_raw_indel_het06_mmq30_mbq20_chr10.vcf), (RodBinding name=input11 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/indel/28genome/28genome_raw_indel_het06_mmq30_mbq20_chr11.vcf), (RodBinding name=input12 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/indel/28genome/28genome_raw_indel_het06_mmq30_mbq20_chr12.vcf), (RodBinding name=input13 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/indel/28genome/28genome_raw_indel_het06_mmq30_mbq20_chr13.vcf), (RodBinding name=input14 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/indel/28genome/28genome_raw_indel_het06_mmq30_mbq20_chr14.vcf), (RodBinding name=input15 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/indel/28genome/28genome_raw_indel_het06_mmq30_mbq20_chr15.vcf), (RodBinding name=input16 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/indel/28genome/28genome_raw_indel_het06_mmq30_mbq20_chr16.vcf), (RodBinding name=input17 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/indel/28genome/28genome_raw_indel_het06_mmq30_mbq20_chr17.vcf), (RodBinding name=input18 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/indel/28genome/28genome_raw_indel_het06_mmq30_mbq20_chr18.vcf), (RodBinding name=input19 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/indel/28genome/28genome_raw_indel_het06_mmq30_mbq20_chr19.vcf), (RodBinding name=input20 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/indel/28genome/28genome_raw_indel_het06_mmq30_mbq20_chr20.vcf), (RodBinding name=inputX source=/groupvol/pgm/home/satanur/analysis/2012_02_28/indel/28genome/28genome_raw_indel_het06_mmq30_mbq20_chrX.vcf), (RodBinding name=inputUn source=/groupvol/pgm/home/satanur/analysis/2012_02_28/indel/28genome/28genome_raw_indel_het06_mmq30_mbq20_chrUn.vcf), (RodBinding name=inputR source=/groupvol/pgm/home/satanur/analysis/2012_02_28/indel/28genome/28genome_raw_indel_het06_mmq30_mbq20_chr_random.vcf)] out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub genotypemergeoption=PRIORITIZE filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED rod_priority_list=inputM,input1,input2,input3,input4,input5,input6,input7,input8,input9,input10,input11,input12,input13,input14,input15,input16,input17,input18,input19,input20,inputX,inputUn,inputR printComplexMerges=false filteredAreUncalled=false minimalVCF=false setKey=set assumeIdenticalSamples=false minimumN=1 mergeInfoWithMaxAC=false filter_mismatching_base_and_quals=false" ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/groupvol/pgm/home/satanur/rat_genomes/bwa/wky/2010-11-22/mapping/WKY_samtools_merge_clean_fix_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/lew_kh_non_phix_reads/2011-01-07/mapping/LEW_samtools_merge_clean_fix_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/shr_non_phix_reads/2011-01-07/mapping/SHR_samtools_merge_clean_fix_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/gk/2010-11-22/mapping/GK_samtools_merge_clean_fix_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bfast/bn_lx_fragment_bfast/2011-02-01/mapping/BN.Lx_picard_merge_clean_recal_CMQ.bam, /groupvol/pgm/home/satanur/rat_genomes/bfast/eve_fragment_bfast/2011-10-31/mapping/EVE_picard_merge_clean_recal_CMQ.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/f344/2011-04-01/mapping/F344_Ncrl_samtools_merge_markdup_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/ss/2011-04-01/mapping/SS_JR_samtools_merge_markdup_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/sr/2011-04-01/mapping/SR_JR_samtools_merge_markdup_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/shr_us/2011-04-01/mapping/SHR_NHSD_samtools_merge_markdup_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/lew_us/2011-04-01/mapping/LEW_NCRLBR_samtools_merge_markdup_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/wky_gla/2011-08-02/mapping/WKY_Gla_samtools_merge_markdup_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/shrsp_gla/2011-09-21/mapping/SHRSP_Gla_samtools_merge_markdup_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/ss_jrmcwi_hiseq/2012-02-16/mapping/SS_JRHSDMCWI_samtools_merge_markdup_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/fhh/2011-10-06/mapping/FHH_samtools_merge_markdup_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/fhl/2012-01-03/mapping/FHL_samtools_merge_markdup_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/mhs/2011-11-16/mapping/MHS_samtools_merge_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/mns/2011-11-16/mapping/MNS_samtools_merge_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/le_stm/2011-11-16/mapping/LE_samtools_merge_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/lh/2011-11-18/mapping/LH_samtools_merge_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/ln/2011-11-19/mapping/LN_samtools_merge_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/ll/2011-11-18/mapping/LL_samtools_merge_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/aci/2012-01-11/mapping/ACI_samtools_merge_markdup_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/sbh/2012-02-16/mapping/SBH_samtools_merge_markdup_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/sbn/2012-02-16/mapping/SBN_samtools_merge_markdup_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/bbdp/2012-02-22/mapping/BBDP_markdup_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/wag/2012-02-22/mapping/WAG_markdup_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/wky_nhsd/2012-02-22/mapping/WKY_NHSD_markdup_clean_recal.bam] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[chr19] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/tmp/pbs.988884.cx1b/tmp_reference.fa rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=4 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=INDEL p_nonref_model=EXACT heterozygosity=1.0E-6 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=10.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) min_base_quality_score=17 max_deletion_fraction=0.05 multiallelic=false max_alternate_alleles=5 min_indel_count_for_genotyping=4 indel_heterozygosity=1.0E-6 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 bandedIndel=false indelDebug=false ignoreSNPAlleles=false dbsnp=(RodBinding name=dbsnp source=/home/satanur/dbsnp/dbsnp_125_rn34.vcf) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[DepthOfCoverage, AlleleBalance, HomopolymerRun, QualByDepth, MappingQualityRankSumTest, ReadPosRankSumTest, HaplotypeScore] excludeAnnotation=[] filter_mismatching_base_and_quals=false" ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##reference=file:///tmp/pbs.988884.cx1b/tmp_reference.fa ##reference=file:///tmp/pbs.992103.cx1b/tmp_reference.fa ##reference=file:///tmp/pbs.995595.cx1b/tmp_reference.fa CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ACI BBDP BN.Lx EVE F344/Ncrl FHH FHL GK LE/Stm LEW LEW/NcrlBR LH LL LN MHS MNS SBH SBN SHR SHR/NHsd SHRSP/Gla SR/Jr SS/Jr SS_JRHSDMCWI WAG WKY WKY/Gla WKY_NHSD 2. 28genome_SNP_part1.vcf.gz and 28genome_SNP_part2.vcf.gz ##fileformat=VCFv4.1 ##ApplyRecalibration="analysis_type=ApplyRecalibration input_file=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/tmp/pbs.991320.cx1b/tmp_reference.fa rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null help=false input=[(RodBinding name=input source=/groupvol/pgm/home/satanur/analysis/2012_02_28/snp/28genome/28genome_raw_snp_het06_mmq30_mbq20.vcf)] recal_file=/groupvol/pgm/home/satanur/analysis/2012_02_28/snp/28genome/variant_recal/28genome_raw_SNP_10guassian_t30.recal tranches_file=/groupvol/pgm/home/satanur/analysis/2012_02_28/snp/28genome/variant_recal/28genome_raw_SNP_10guassian_t30.tranches out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub ts_filter_level=99.0 ignore_filter=null mode=SNP filter_mismatching_base_and_quals=false" ##CombineVariants="analysis_type=CombineVariants input_file=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/tmp/pbs.989904.cx1b/tmp_reference.fa rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null help=false variant=[(RodBinding name=inputM source=/groupvol/pgm/home/satanur/analysis/2012_02_28/snp/28genome/28genome_raw_snp_het06_mmq30_mbq20_chrM.vcf), (RodBinding name=input1 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/snp/28genome/28genome_raw_snp_het06_mmq30_mbq20_chr1.vcf), (RodBinding name=input2 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/snp/28genome/28genome_raw_snp_het06_mmq30_mbq20_chr2.vcf), (RodBinding name=input3 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/snp/28genome/28genome_raw_snp_het06_mmq30_mbq20_chr3.vcf), (RodBinding name=input4 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/snp/28genome/28genome_raw_snp_het06_mmq30_mbq20_chr4.vcf), (RodBinding name=input5 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/snp/28genome/28genome_raw_snp_het06_mmq30_mbq20_chr5.vcf), (RodBinding name=input6 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/snp/28genome/28genome_raw_snp_het06_mmq30_mbq20_chr6.vcf), (RodBinding name=input7 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/snp/28genome/28genome_raw_snp_het06_mmq30_mbq20_chr7.vcf), (RodBinding name=input8 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/snp/28genome/28genome_raw_snp_het06_mmq30_mbq20_chr8.vcf), (RodBinding name=input9 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/snp/28genome/28genome_raw_snp_het06_mmq30_mbq20_chr9.vcf), (RodBinding name=input10 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/snp/28genome/28genome_raw_snp_het06_mmq30_mbq20_chr10.vcf), (RodBinding name=input11 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/snp/28genome/28genome_raw_snp_het06_mmq30_mbq20_chr11.vcf), (RodBinding name=input12 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/snp/28genome/28genome_raw_snp_het06_mmq30_mbq20_chr12.vcf), (RodBinding name=input13 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/snp/28genome/28genome_raw_snp_het06_mmq30_mbq20_chr13.vcf), (RodBinding name=input14 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/snp/28genome/28genome_raw_snp_het06_mmq30_mbq20_chr14.vcf), (RodBinding name=input15 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/snp/28genome/28genome_raw_snp_het06_mmq30_mbq20_chr15.vcf), (RodBinding name=input16 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/snp/28genome/28genome_raw_snp_het06_mmq30_mbq20_chr16.vcf), (RodBinding name=input17 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/snp/28genome/28genome_raw_snp_het06_mmq30_mbq20_chr17.vcf), (RodBinding name=input18 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/snp/28genome/28genome_raw_snp_het06_mmq30_mbq20_chr18.vcf), (RodBinding name=input19 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/snp/28genome/28genome_raw_snp_het06_mmq30_mbq20_chr19.vcf), (RodBinding name=input20 source=/groupvol/pgm/home/satanur/analysis/2012_02_28/snp/28genome/28genome_raw_snp_het06_mmq30_mbq20_chr20.vcf), (RodBinding name=inputX source=/groupvol/pgm/home/satanur/analysis/2012_02_28/snp/28genome/28genome_raw_snp_het06_mmq30_mbq20_chrX.vcf), (RodBinding name=inputUn source=/groupvol/pgm/home/satanur/analysis/2012_02_28/snp/28genome/28genome_raw_snp_het06_mmq30_mbq20_chrUn.vcf), (RodBinding name=inputR source=/groupvol/pgm/home/satanur/analysis/2012_02_28/snp/28genome/28genome_raw_snp_het06_mmq30_mbq20_chr_random.vcf)] out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub genotypemergeoption=PRIORITIZE filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED rod_priority_list=inputM,input1,input2,input3,input4,input5,input6,input7,input8,input9,input10,input11,input12,input13,input14,input15,input16,input17,input18,input19,input20,inputX,inputUn,inputR printComplexMerges=false filteredAreUncalled=false minimalVCF=false setKey=set assumeIdenticalSamples=false minimumN=1 mergeInfoWithMaxAC=false filter_mismatching_base_and_quals=false" ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/groupvol/pgm/home/satanur/rat_genomes/bwa/wky/2010-11-22/mapping/WKY_samtools_merge_clean_fix_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/lew_kh_non_phix_reads/2011-01-07/mapping/LEW_samtools_merge_clean_fix_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/shr_non_phix_reads/2011-01-07/mapping/SHR_samtools_merge_clean_fix_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/gk/2010-11-22/mapping/GK_samtools_merge_clean_fix_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bfast/bn_lx_fragment_bfast/2011-02-01/mapping/BN.Lx_picard_merge_clean_recal_CMQ.bam, /groupvol/pgm/home/satanur/rat_genomes/bfast/eve_fragment_bfast/2011-10-31/mapping/EVE_picard_merge_clean_recal_CMQ.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/f344/2011-04-01/mapping/F344_Ncrl_samtools_merge_markdup_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/ss/2011-04-01/mapping/SS_JR_samtools_merge_markdup_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/sr/2011-04-01/mapping/SR_JR_samtools_merge_markdup_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/shr_us/2011-04-01/mapping/SHR_NHSD_samtools_merge_markdup_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/lew_us/2011-04-01/mapping/LEW_NCRLBR_samtools_merge_markdup_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/wky_gla/2011-08-02/mapping/WKY_Gla_samtools_merge_markdup_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/shrsp_gla/2011-09-21/mapping/SHRSP_Gla_samtools_merge_markdup_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/ss_jrmcwi_hiseq/2012-02-16/mapping/SS_JRHSDMCWI_samtools_merge_markdup_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/fhh/2011-10-06/mapping/FHH_samtools_merge_markdup_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/fhl/2012-01-03/mapping/FHL_samtools_merge_markdup_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/mhs/2011-11-16/mapping/MHS_samtools_merge_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/mns/2011-11-16/mapping/MNS_samtools_merge_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/le_stm/2011-11-16/mapping/LE_samtools_merge_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/lh/2011-11-18/mapping/LH_samtools_merge_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/ln/2011-11-19/mapping/LN_samtools_merge_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/ll/2011-11-18/mapping/LL_samtools_merge_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/aci/2012-01-11/mapping/ACI_samtools_merge_markdup_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/sbh/2012-02-16/mapping/SBH_samtools_merge_markdup_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/sbn/2012-02-16/mapping/SBN_samtools_merge_markdup_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/bbdp/2012-02-22/mapping/BBDP_markdup_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/wag/2012-02-22/mapping/WAG_markdup_clean_recal.bam, /groupvol/pgm/home/satanur/rat_genomes/bwa/wky_nhsd/2012-02-22/mapping/WKY_NHSD_markdup_clean_recal.bam] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[chr19] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/tmp/pbs.988860.cx1b/tmp_reference.fa rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=RECALCULATE baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=4 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=SNP p_nonref_model=EXACT heterozygosity=1.0E-6 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=10.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) min_base_quality_score=17 max_deletion_fraction=0.05 multiallelic=false max_alternate_alleles=5 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 bandedIndel=false indelDebug=false ignoreSNPAlleles=false dbsnp=(RodBinding name=dbsnp source=/home/satanur/dbsnp/dbsnp_125_rn34.vcf) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[DepthOfCoverage, AlleleBalance, HomopolymerRun, QualByDepth, MappingQualityRankSumTest, ReadPosRankSumTest, HaplotypeScore] excludeAnnotation=[] filter_mismatching_base_and_quals=false" ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##reference=file:///tmp/pbs.988860.cx1b/tmp_reference.fa ##reference=file:///tmp/pbs.989904.cx1b/tmp_reference.fa ##reference=file:///tmp/pbs.991320.cx1b/tmp_reference.fa CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ACI BBDP BN.Lx EVE F344/Ncrl FHH FHL GK LE/Stm LEW LEW/NcrlBR LH LL LN MHS MNS SBH SBN SHR SHR/NHsd SHRSP/Gla SR/Jr SS/Jr SS_JRHSDMCWI WAG WKY WKY/Gla WKY_NHSD