Mercurial > repos > malex > bayesase
view test-data/update_genomes_test_data/W55_snp_testGenes.vcf @ 0:e979cb57a5d5 draft default tip
"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
| author | malex |
|---|---|
| date | Thu, 14 Jan 2021 21:51:36 +0000 |
| parents | |
| children |
line wrap: on
line source
##fileformat=VCFv4.2 ##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location"> ##FILTER=<ID=Het,Description="isHet == 1"> ##FILTER=<ID=LowQual,Description="Low quality"> ##FILTER=<ID=PASS,Description="All filters passed"> ##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=FT,Number=.,Type=String,Description="Genotype-level filter"> ##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=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=3.2-2-gec30cee,Date="Fri Aug 22 11:38:29 PDT 2014",Epoch=1408732709322,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=/home/rcf-40/msalomon/cmb/CEGS_fly_sequencing/reference/dmel-all-chromosome-r5.41_edited_headers.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 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=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/DGRP_48.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant2 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/DGRP_382.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant3 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/DGRP_385.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant4 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/DGRP_390.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant5 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/DGRP_395.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant6 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/DGRP_397.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant7 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/DGRP_505.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant8 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/DGRP_528.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant9 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/DGRP_530.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant10 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/DGRP_551.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant11 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/DGRP_559.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant12 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/DGRP_566.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant13 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/DGRP_596.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant14 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/DGRP_627.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant15 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/DGRP_630.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant16 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/DGRP_634.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant17 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/DGRP_748.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant18 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/DGRP_819.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant19 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/DGRP_843.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant20 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/DGRP_849.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant21 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/DGRP_913.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant22 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_21.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant23 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_26.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant24 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_28.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant25 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_38.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant26 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_40.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant27 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_41.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant28 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_42.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant29 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_45.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant30 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_49.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant31 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_57.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant32 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_59.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant33 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_69.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant34 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_73.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant35 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_75.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant36 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_83.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant37 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_85.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant38 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_88.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant39 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_91.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant40 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_93.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant41 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_101.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant42 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_105.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant43 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_109.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant44 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_129.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant45 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_136.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant46 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_138.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant47 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_142.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant48 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_149.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant49 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_153.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant50 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_158.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant51 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_161.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant52 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_176.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant53 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_177.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant54 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_181.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant55 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_195.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant56 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_208.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant57 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_217.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant58 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_227.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant59 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_228.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant60 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_229.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant61 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_233.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant62 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_235.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant63 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_237.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant64 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_239.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant65 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_256.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant66 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_272.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant67 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_280.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant68 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_287.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant69 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_301.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant70 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_303.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant71 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_304.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant72 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_307.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant73 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_309.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant74 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_310.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant75 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_313.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant76 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_315.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant77 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_317.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant78 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_318.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant79 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_320.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant80 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_321.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant81 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_324.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant82 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_325.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant83 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_332.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant84 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_335.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant85 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_336.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant86 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_338.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant87 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_340.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant88 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_350.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant89 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_352.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant90 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_356.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant91 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_357.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant92 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_358.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant93 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_359.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant94 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_360.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant95 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_361.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant96 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_362.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant97 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_365.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant98 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_367.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant99 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_370.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant100 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_371.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant101 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_373.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant102 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_374.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant103 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_375.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant104 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_377.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant105 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_378.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant106 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_379.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant107 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_380.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant108 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_381.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant109 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_383.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant110 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_386.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant111 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_391.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant112 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_392.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant113 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_398.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant114 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_399.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant115 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_405.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant116 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_406.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant117 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_409.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant118 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_426.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant119 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_427.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant120 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_437.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant121 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_439.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant122 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_440.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant123 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_441.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant124 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_443.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant125 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_461.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant126 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_486.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant127 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_491.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant128 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_492.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant129 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_502.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant130 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_508.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant131 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_509.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant132 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_513.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant133 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_517.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant134 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_531.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant135 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_535.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant136 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_554.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant137 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_555.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant138 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_563.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant139 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_584.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant140 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_589.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant141 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_591.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant142 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_595.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant143 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_639.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant144 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_642.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant145 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_646.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant146 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_703.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant147 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_705.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant148 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_707.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant149 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_712.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant150 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_714.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant151 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_716.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant152 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_721.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant153 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_727.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant154 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_730.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant155 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_732.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant156 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_737.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant157 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_738.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant158 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_757.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant159 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_761.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant160 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_765.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant161 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_774.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant162 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_776.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant163 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_783.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant164 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_786.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant165 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_787.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant166 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_790.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant167 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_796.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant168 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_799.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant169 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_801.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant170 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_802.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant171 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_804.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant172 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_805.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant173 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_808.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant174 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_810.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant175 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_812.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant176 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_818.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant177 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_820.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant178 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_821.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant179 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_822.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant180 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_832.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant181 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_837.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant182 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_850.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant183 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_852.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant184 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_853.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant185 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_855.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant186 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_857.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant187 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_859.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant188 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_861.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant189 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_879.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant190 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_882.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant191 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_884.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant192 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_887.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant193 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_890.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant194 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_892.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant195 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_894.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant196 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_897.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant197 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_900.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant198 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_907.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant199 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_908.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant200 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Raleigh_911.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant201 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/w1118.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant202 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_23.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant203 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_26.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant204 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_33.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant205 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_34.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant206 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_35.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant207 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_36.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant208 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_37.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant209 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_38.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant210 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_40.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant211 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_43.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant212 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_47.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant213 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_49.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant214 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_50.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant215 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_52.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant216 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_54.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant217 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/W55.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant218 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_56.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant219 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_59.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant220 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_60.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant221 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_62.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant222 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_63.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant223 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_64.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant224 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_66.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant225 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_67.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant226 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_68.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant227 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_69.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant228 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_70.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant229 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_74.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant230 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_76.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant231 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_79.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant232 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_80.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant233 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_82.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant234 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_84.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant235 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_86.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant236 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_87.raw.SNPs.and.indels.g.vcf)]), (RodBindingCollection [(RodBinding name=variant237 source=/home/cmb-07/sn1/msalomon/CEGS_HaplotypeCaller/g_vcfs/Winters_114.raw.SNPs.and.indels.g.vcf)])] out=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub bcf=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=30.0 max_alternate_alleles=6 input_prior=[] sample_ploidy=2 annotation=[InbreedingCoeff, FisherStrand, QualByDepth, ChromosomeCounts, GenotypeSummaries] 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,CommandLine="SelectVariants --output /ufrc/mcintyre/share/BASE_mclab/galaxy/vcf_by_genotype/W55_snp.vcf --sample-name W55 --exclude-non-variants true --variant /ufrc/mcintyre/share/mel_cegs_variant_info/vcf_files_v3/CEGS.237.lines.SNPs.filtered.set.1.recode.vcf --reference /ufrc/mcintyre/share/references/dmel_fb551/dmel-all-chromosome-r5.51.fasta --invertSelect 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="4.1.4.0",Date="July 22, 2020 1:46:33 PM EDT"> ##GVCFBlock=minGQ=0(inclusive),maxGQ=5(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"> ##SelectVariants="analysis_type=SelectVariants input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/Users/msalomon/Desktop/reference/dmel-all-chromosome-r5.41_edited_headers.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 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=8 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 logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=CEGS.ALL.snp.and.indel.raw.HETS.marked.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.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_mismatching_base_and_quals=false filter_bases_not_stored=false" ##VariantFiltration="analysis_type=VariantFiltration input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/Users/msalomon/Desktop/reference/dmel-all-chromosome-r5.41_edited_headers.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 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=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 logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=CEGS.ALL.snp.and.indel.raw.vcf) mask=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub filterExpression=[] filterName=[] genotypeFilterExpression=[isHet == 1] genotypeFilterName=[Het] clusterSize=3 clusterWindowSize=0 maskExtension=0 maskName=Mask filterNotInMask=false missingValuesInExpressionsShouldEvaluateAsFailing=false invalidatePreviousFilters=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false" ##bcftools_viewCommand=view -O v -o /ufrc/mcintyre/share/mel_cegs_variant_info/vcf_files_v3/CEGS.237.lines.SNPs.filtered.set.1.recode.vcf /ufrc/mcintyre/share/mel_cegs_variant_info/vcf_files_v3/CEGS.237.lines.SNPs.filtered.set.1.recode.vcf.gz; Date=Wed Jul 22 13:40:32 2020 ##bcftools_viewVersion=1.10.2+htslib-1.10.2 ##contig=<ID=YHet,length=347038,assembly=dmel-all-chromosome-r5.51.fasta> ##contig=<ID=dmel_mitochondrion_genome,length=19517,assembly=dmel-all-chromosome-r5.51.fasta> ##contig=<ID=2L,length=23011544,assembly=dmel-all-chromosome-r5.51.fasta> ##contig=<ID=X,length=22422827,assembly=dmel-all-chromosome-r5.51.fasta> ##contig=<ID=3L,length=24543557,assembly=dmel-all-chromosome-r5.51.fasta> ##contig=<ID=4,length=1351857,assembly=dmel-all-chromosome-r5.51.fasta> ##contig=<ID=2R,length=21146708,assembly=dmel-all-chromosome-r5.51.fasta> ##contig=<ID=3R,length=27905053,assembly=dmel-all-chromosome-r5.51.fasta> ##contig=<ID=Uextra,length=29004656,assembly=dmel-all-chromosome-r5.51.fasta> ##contig=<ID=2RHet,length=3288761,assembly=dmel-all-chromosome-r5.51.fasta> ##contig=<ID=2LHet,length=368872,assembly=dmel-all-chromosome-r5.51.fasta> ##contig=<ID=3LHet,length=2555491,assembly=dmel-all-chromosome-r5.51.fasta> ##contig=<ID=3RHet,length=2517507,assembly=dmel-all-chromosome-r5.51.fasta> ##contig=<ID=U,length=10049037,assembly=dmel-all-chromosome-r5.51.fasta> ##contig=<ID=XHet,length=204112,assembly=dmel-all-chromosome-r5.51.fasta> ##reference=file:///ufrc/mcintyre/share/references/dmel_fb551/dmel-all-chromosome-r5.51.fasta ##source=SelectVariants #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT W55 X 7781305 . G C 17318.70 PASS AC=2;AF=1.00;AN=2;DP=3 GT:AD:DP:GQ:PL 1/1:0,3:3:9:135,9,0 X 7782104 . T C 18004.60 PASS AC=2;AF=1.00;AN=2;DP=6 GT:AD:DP:GQ:PL 1/1:3,0:6:18:270,18,0 X 7782113 . A G 18014.90 PASS AC=2;AF=1.00;AN=2;DP=7 GT:AD:DP:GQ:PL 1/1:7,21:7:21:78,21,0 X 7782164 . G A 814.59 PASS AC=2;AF=1.00;AN=2;DP=6 GT:AD:DP:GQ:PL 1/1:0,0:6:18:265,18,0 X 21889635 . C T 30606.60 PASS AC=2;AF=1.00;AN=2;DP=4 GT:AD:DP:GQ:PL 1/1:0,4:4:12:158,12,0 X 21889661 . G C 70712.10 PASS AC=2;AF=1.00;AN=2;DP=4 GT:AD:DP:GQ:PL 1/1:4,0:4:12:0,6,90 X 21889690 . A C 22562.60 PASS AC=2;AF=1.00;AN=2;DP=2 GT:AD:DP:GQ:PL 1/1:0,2:2:9:125,9,0 X 21889694 . G A 68972.30 PASS AC=2;AF=1.00;AN=2;DP=3 GT:AD:DP:GQ:PL 1/1:0,3:3:9:125,9,0 X 21891112 . G T 52288.30 PASS AC=2;AF=1.00;AN=2;DP=7 GT:AD:DP:GQ:PL 1/1:0,7:7:21:300,21,0 X 21891166 . G T 58400.10 PASS AC=2;AF=1.00;AN=2;DP=4 GT:AD:DP:GQ:PL 1/1:0,4:4:12:177,12,0 X 21891357 . T G 30378 PASS AC=2;AF=1.00;AN=2;DP=6 GT:AD:DP:GQ:PL 1/1:0,6:6:18:261,18,0 X 21891602 . A T 53918.40 PASS AC=2;AF=1.00;AN=2;DP=5 GT:AD:DP:GQ:PL 1/1:0,5:5:15:0,15,0 X 21892908 . C G 42352.40 PASS AC=2;AF=1.00;AN=2;DP=2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 X 21893288 . C T 80065.60 PASS AC=2;AF=1.00;AN=2;DP=3 GT:AD:DP:GQ:PL 1/1:0,3:3:9:135,9,0 X 21893289 . T G 80753.10 PASS AC=2;AF=1.00;AN=2;DP=3 GT:AD:DP:GQ:PL 1/1:0,3:3:9:135,9,0 X 21893294 . T A 80892.60 PASS AC=2;AF=1.00;AN=2;DP=3 GT:AD:DP:GQ:PL 1/1:0,3:3:9:135,9,0 X 21893803 . C T 58173.10 PASS AC=2;AF=1.00;AN=2;DP=7 GT:AD:DP:GQ:PL 1/1:0,7:7:21:272,21,0 X 21894302 . T A 71351.10 PASS AC=2;AF=1.00;AN=2;DP=6 GT:AD:DP:GQ:PL 1/1:0,6:6:18:263,18,0 X 21895556 . A G 107863 PASS AC=2;AF=1.00;AN=2;DP=5 GT:AD:DP:GQ:PL 1/1:0,5:5:15:222,15,0 X 21895697 . T C 110094 PASS AC=2;AF=1.00;AN=2;DP=5 GT:AD:DP:GQ:PL 1/1:0,5:5:15:218,15,0 X 21895821 . G C 54704.80 PASS AC=2;AF=1.00;AN=2;DP=4 GT:AD:DP:GQ:PL 1/1:0,4:4:12:99,12,0 X 21895843 . G C 68444.20 PASS AC=2;AF=1.00;AN=2;DP=4 GT:AD:DP:GQ:PL 1/1:0,6:4:12:0,6,0 X 21896261 . A T 63913.60 PASS AC=2;AF=1.00;AN=2;DP=5 GT:AD:DP:GQ:PL 1/1:0,5:5:15:225,15,0 X 21896263 . A G 73066.20 PASS AC=2;AF=1.00;AN=2;DP=5 GT:AD:DP:GQ:PL 1/1:0,5:5:15:225,15,0 X 21896622 . G A 6171.18 PASS AC=2;AF=1.00;AN=2;DP=3 GT:AD:DP:GQ:PL 1/1:0,3:3:9:135,9,0 X 21896626 . G A 6861.15 PASS AC=2;AF=1.00;AN=2;DP=2 GT:AD:DP:GQ:PL 1/1:0,0:2:9:135,9,0 X 21897553 . T C 84267.90 PASS AC=2;AF=1.00;AN=2;DP=6 GT:AD:DP:GQ:PL 1/1:0,6:6:18:260,18,0 X 21898641 . T C 66103.40 PASS AC=2;AF=1.00;AN=2;DP=3 GT:AD:DP:GQ:PL 1/1:0,3:3:9:131,9,0 X 21898891 . T C 39137.80 PASS AC=2;AF=1.00;AN=2;DP=2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:55,0,0 X 21898907 . G T 32494.10 PASS AC=2;AF=1.00;AN=2;DP=3 GT:AD:DP:GQ:PL 1/1:0,33:3:9:135,9,0 X 21898915 . A C 45022.10 PASS AC=2;AF=1.00;AN=2;DP=3 GT:AD:DP:GQ:PL 1/1:0,3:3:9:135,9,0 X 21898931 . G A 27838.70 PASS AC=2;AF=1.00;AN=2;DP=2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:55,6,0 X 21899027 . T G 42283.40 PASS AC=2;AF=1.00;AN=2;DP=2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:73,6,0 X 21899043 . T A 61169.20 PASS AC=2;AF=1.00;AN=2;DP=2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:67,6,0 X 21899576 . C T 83305.10 PASS AC=2;AF=1.00;AN=2;DP=3 GT:AD:DP:GQ:PL 1/1:0,3:3:9:123,9,0 X 21899675 . T C 139002 PASS AC=2;AF=1.00;AN=2;DP=4 GT:AD:DP:GQ:PL 1/1:0,4:4:12:172,12,0 X 21900298 . C T 40553.90 PASS AC=2;AF=1.00;AN=2;DP=6 GT:AD:DP:GQ:PL 1/1:0,6:6:18:270,18,0 X 21900307 . A G 80133.80 PASS AC=2;AF=1.00;AN=2;DP=8 GT:AD:DP:GQ:PL 1/1:0,8:8:24:351,24,0 X 21902804 . C T 75910.80 PASS AC=2;AF=1.00;AN=2;DP=4 GT:AD:DP:GQ:PL 1/1:0,4:4:12:173,12,0 X 21902864 . G A 62085.10 PASS AC=2;AF=1.00;AN=2;DP=4 GT:AD:DP:GQ:PL 1/1:0,4:4:12:180,12,0 X 21902872 . T A 83073.30 PASS AC=2;AF=1.00;AN=2;DP=5 GT:AD:DP:GQ:PL 1/1:0,5:5:15:224,15,0 X 21903096 . G A 40162.90 PASS AC=2;AF=1.00;AN=2;DP=5 GT:AD:DP:GQ:PL 1/1:0,5:5:15:193,15,0 X 21905664 . A C 34889.80 PASS AC=2;AF=1.00;AN=2;DP=4 GT:AD:DP:GQ:PL 1/1:0,4:4:12:180,12,0 X 21905680 . T G 65074.20 PASS AC=2;AF=1.00;AN=2;DP=4 GT:AD:DP:GQ:PL 1/1:0,4:4:12:180,12,0 X 21907863 . A T 10377.10 PASS AC=2;AF=1.00;AN=2;DP=3 GT:AD:DP:GQ:PL 1/1:0,3:3:9:118,9,0 X 21907941 . G A 24422.20 PASS AC=2;AF=1.00;AN=2;DP=3 GT:AD:DP:GQ:PL 1/1:0,3:3:9:127,9,0 X 21908562 . G T 28433.80 PASS AC=2;AF=1.00;AN=2;DP=2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 X 21908564 . T A 26478.90 PASS AC=2;AF=1.00;AN=2;DP=2 GT:AD:DP:GQ:PL 1/1:0,2:2:9:131,9,0 X 21908576 . T C 26077.20 PASS AC=2;AF=1.00;AN=2;DP=3 GT:AD:DP:GQ:PL 1/1:0,3:3:9:131,9,0 X 21908620 . T C 23001.60 PASS AC=2;AF=1.00;AN=2;DP=2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:87,6,0 X 21909429 . A C 9195.76 PASS AC=2;AF=1.00;AN=2;DP=6 GT:AD:DP:GQ:PL 1/1:0,6:6:18:270,18,0 2R 13755520 . A T 127979 PASS AC=2;AF=1.00;AN=2;DP=3 GT:AD:DP:GQ:PL 1/1:0,24:3:9:1027,75,0 2R 13755788 . A C 119974 PASS AC=2;AF=1.00;AN=2;DP=2 GT:AD:DP:GQ:PL 1/1:0,2:2:6:90,6,0 2R 13758421 . C T 25254.50 PASS AC=2;AF=1.00;AN=2;DP=4 GT:AD:DP:GQ:PL 1/1:0,4:4:12:149,12,0 2R 13759577 . A G 150046 PASS AC=2;AF=1.00;AN=2;DP=5 GT:AD:DP:GQ:PL 1/1:0,5:5:15:221,15,0 2R 16207027 . C T 74656.50 PASS AC=2;AF=1.00;AN=2;DP=6 GT:AD:DP:GQ:PL 1/1:0,6:6:18:270,18,0 2R 16207500 . A C 132895 PASS AC=2;AF=1.00;AN=2;DP=3 GT:AD:DP:GQ:PL 1/1:0,6:3:9:0,21,249 2R 16207580 . G C 139267 PASS AC=2;AF=1.00;AN=2;DP=5 GT:AD:DP:GQ:PL 1/1:0,5:5:15:213,15,0 2R 16208634 . T C 141438 PASS AC=2;AF=1.00;AN=2;DP=6 GT:AD:DP:GQ:PL 1/1:0,6:6:18:268,18,0 2R 16209380 . T A 180650 PASS AC=2;AF=1.00;AN=2;DP=8 GT:AD:DP:GQ:PL 1/1:9,8:8:24:0,21,303 2R 16209465 . C T 150905 PASS AC=2;AF=1.00;AN=2;DP=4 GT:AD:DP:GQ:PL 1/1:0,4:4:12:0,21,306 2R 16209499 . T C 124518 PASS AC=2;AF=1.00;AN=2;DP=3 GT:AD:DP:GQ:PL 1/1:0,3:3:9:13,0,0 2R 16209697 . T C 121720 PASS AC=2;AF=1.00;AN=2;DP=8 GT:AD:DP:GQ:PL 1/1:0,0:8:24:353,24,0 2R 16210686 . A C 141265 PASS AC=2;AF=1.00;AN=2;DP=3 GT:AD:DP:GQ:PL 1/1:10,0:3:9:7,0,0 2R 16210895 . C T 102435 PASS AC=2;AF=1.00;AN=2;DP=5 GT:AD:DP:GQ:PL 1/1:0,5:5:15:219,15,0 2R 16210940 . C G 97625.90 PASS AC=2;AF=1.00;AN=2;DP=6 GT:AD:DP:GQ:PL 1/1:0,6:6:18:36,0,0 2R 16211042 . A G 95462 PASS AC=2;AF=1.00;AN=2;DP=9 GT:AD:DP:GQ:PL 1/1:0,9:9:27:339,36,0 2R 16211202 . C T 129728 PASS AC=2;AF=1.00;AN=2;DP=7 GT:AD:DP:GQ:PL 1/1:0,7:7:21:303,21,0 2R 16211857 . T C 143370 PASS AC=2;AF=1.00;AN=2;DP=8 GT:AD:DP:GQ:PL 1/1:0,8:8:24:0,60,900 2R 16212083 . C G 148987 PASS AC=2;AF=1.00;AN=2;DP=5 GT:AD:DP:GQ:PL 1/1:0,5:5:15:223,15,0 2R 16212530 . T C 127450 PASS AC=2;AF=1.00;AN=2;DP=9 GT:AD:DP:GQ:PL 1/1:0,6:9:27:391,27,0 2R 16212536 . T G 125381 PASS AC=2;AF=1.00;AN=2;DP=7 GT:AD:DP:GQ:PL 1/1:0,7:7:21:5,0,0 2R 16212827 . A G 157750 PASS AC=2;AF=1.00;AN=2;DP=6 GT:AD:DP:GQ:PL 1/1:0,6:6:18:0,30,0 2R 16213511 . T C 104278 PASS AC=2;AF=1.00;AN=2;DP=6 GT:AD:DP:GQ:PL 1/1:0,0:6:18:1,5,0