| Previous changeset 2:3be27a9a7313 (2020-04-10) Next changeset 4:1cea23583655 (2020-08-14) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 7297efcf34a6262434c6b0f41243fbcb1947af80" |
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modified:
gatk4_Mutect2.xml macros.xml test-data/Mutect2-out1.vcf test-data/Mutect2-out2.vcf test-data/Mutect2-out3.vcf test-data/Mutect2-out4.vcf test-data/Mutect2-out5-1.tabular test-data/Mutect2-out5.bam test-data/Mutect2-out5.vcf |
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added:
test-data/Mutect2-out6.vcf test-data/chr20.fa test-data/normal.bam test-data/tumor.bam |
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removed:
test-data/Mutect2-out5-2.tabular |
| b |
| diff -r 3be27a9a7313 -r 287c4af133e6 gatk4_Mutect2.xml --- a/gatk4_Mutect2.xml Fri Apr 10 14:10:55 2020 -0400 +++ b/gatk4_Mutect2.xml Sun May 10 17:58:00 2020 -0400 |
| [ |
| b'@@ -9,7 +9,8 @@\n <![CDATA[\n #include source=$set_sections#\n #include source=$pre_gatk_excl_ints_chth#\n- #include source=$bam_index_pre_chth#\n+ #include source=$tumor_bam_index_pre_chth#\n+ #include source=$normal_bam_index_pre_chth#\n #include source=$pre_gatk_ints_chth#\n \n #set ref_flag=\'--reference="reference.fa"\'\n@@ -27,9 +28,6 @@\n #end if\n \n #if str($outputs.output_parameters) == \'yes\'\n- #if str($outputs.debug_activity) == \'yes\'\n- ln -s \'$activity_profile_out\' activity-profile.tab &&\n- #end if\n #if str($outputs.debug_assembly) == \'yes\'\n ln -s \'$assembly_region_out\' assembly-region.tab &&\n #end if\n@@ -38,7 +36,7 @@\n #end if\n #end if\n \n- gatk GetSampleName --input="input.bam" --output="samplename.txt" &&\n+ gatk GetSampleName --input="tumor.bam" --output="samplename.txt" &&\n sample=`cat samplename.txt | sed \'s/"//g\'` &&\n \n #if str($optional.optional_parameters) == \'yes\'\n@@ -78,7 +76,12 @@\n \n gatk Mutect2 --QUIET $ref_flag --tumor-sample "\\$sample"\n \n- #include source=$gatk_bam_input#\n+ #if str($mode.mode_parameters) == \'tumor_only\'\n+ #include source=$gatk_tumor_bam_input#\n+ #else\n+ #include source=$gatk_tumor_bam_input#\n+ #include source=$gatk_normal_bam_input#\n+ #end if\n \n ## OPTIONAL PARAMETERS ##\n \n@@ -222,7 +225,7 @@\n #if $advanced.max_unpruned_variants\n --max-unpruned-variants="$advanced.max_unpruned_variants"\n #end if\n-\n+ --allele-informative-reads-overlap-margin=="$advanced.allele_informative_reads_overlap_margin"\n --active-probability-threshold="$advanced.active_probability_threshold"\n --assembly-region-padding="$advanced.assembly_region_padding"\n --bam-writer-type="$advanced.bam_writer_type"\n@@ -247,7 +250,6 @@\n $advanced.disable_tool_default_annotations\n $advanced.disable_tool_default_read_filters\n $advanced.dont_increase_kmer_sizes_for_cycles\n- $advanced.dont_trim_active_regions\n $advanced.dont_use_soft_clipped_bases\n $advanced.enable_all_annotations\n $advanced.force_active\n@@ -263,9 +265,6 @@\n ## ADDITIONAL OUTPUT PARAMETERS ##\n \n #if str($outputs.output_parameters) == \'yes\'\n- #if str($outputs.debug_activity) == \'yes\'\n- --activity-profile-out="activity-profile.tab"\n- #end if\n #if str($outputs.debug_assembly) == \'yes\'\n --assembly-region-out="assembly-region.tab"\n #end if\n@@ -281,7 +280,19 @@\n ]]>\n </command>\n <inputs>\n- <expand macro="gatk_bam_req_params"/>\n+ <conditional name="mode">\n+ <param name="mode_parameters" type="select" label="Type of analysis">\n+ <option value="tumor_only">Tumor-only</option>\n+ <option value="somatic">Somatic</option>\n+ </param>\n+ <when value="tumor_only">\n+ <expand macro="gatk_tumor_bam_req_params"/>\n+ </when>\n+ <when value="somatic">\n+ <expand macro="gatk_tumor_bam_req_params"/>\n+ <expand macro="gatk_normal_bam_req_params"/>\n+ </when>\n+ </conditional>\n <expand macro="gzip_vcf_params"/>\n <expand macro="ref_sel"/>\n <conditional name="optional">\n@@ -496,6 +507,7 @@\n <option value="yes">Specify parameters</option>\n </param>\n <when value="yes">\n+ <param name="allele_informative_reads_overlap_margin" argument="--allele-informative-reads-overlap-margin" type="integer" optional="true" value="2" label="Likelihood and read-based annotations will only take into consideration reads that overlap the variant or any'..b'in2.bam" />\n+ </conditional>\n <param name="reference_sequence" ftype="fasta" value="reference.fa" />\n <param name="gzipped_output" value="false" />\n <param name="reference_source_selector" value="history" />\n@@ -610,7 +624,10 @@\n <output name="output_vcf" file="Mutect2-out2.vcf" lines_diff="2" />\n </test>\n <test>\n- <param name="input" ftype="bam" value="Mutect2-in3.bam" />\n+ <conditional name="mode">\n+ <param name="mode_parameters" value="tumor_only"/>\n+ <param name="tumor" ftype="bam" value="Mutect2-in3.bam" />\n+ </conditional>\n <param name="reference_sequence" ftype="fasta" value="reference.fa" />\n <param name="gzipped_output" value="false" />\n <param name="reference_source_selector" value="history" />\n@@ -622,18 +639,23 @@\n <output name="output_vcf" file="Mutect2-out3.vcf" lines_diff="2" />\n </test>\n <test>\n- <param name="input" ftype="bam" value="Mutect2-in4.bam" />\n+ <conditional name="mode">\n+ <param name="mode_parameters" value="tumor_only"/>\n+ <param name="tumor" ftype="bam" value="Mutect2-in4.bam" />\n+ </conditional>\n <param name="reference_sequence" ftype="fasta" value="reference.fa" />\n <param name="gzipped_output" value="false" />\n <param name="reference_source_selector" value="history" />\n- <param name="optional_parameters" value="yes" />\n- <param name="advanced_parameters" value="yes" />\n- <param name="dont_trim_active_regions" value="true" />\n+ <param name="optional_parameters" value="no" />\n+ <param name="advanced_parameters" value="no" />\n <param name="output_parameters" value="no" />\n <output name="output_vcf" file="Mutect2-out4.vcf" lines_diff="2" />\n </test>\n <test>\n- <param name="input" ftype="bam" value="Mutect2-in5.bam" />\n+ <conditional name="mode">\n+ <param name="mode_parameters" value="tumor_only"/>\n+ <param name="tumor" ftype="bam" value="Mutect2-in5.bam" />\n+ </conditional>\n <param name="reference_sequence" ftype="fasta" value="reference.fa" />\n <param name="gzipped_output" value="false" />\n <param name="reference_source_selector" value="history" />\n@@ -644,10 +666,23 @@\n <param name="debug_assembly" value="true" />\n <param name="debug_bam" value="true" />\n <output name="output_vcf" file="Mutect2-out5.vcf" lines_diff="2" />\n- <output name="activity_profile_out" file="Mutect2-out5-1.tabular" />\n- <output name="assembly_region_out" file="Mutect2-out5-2.tabular" />\n+ <output name="assembly_region_out" file="Mutect2-out5-1.tabular" />\n <output name="bam_output" file="Mutect2-out5.bam" />\n </test>\n+ <test>\n+ <conditional name="mode">\n+ <param name="mode_parameters" value="somatic"/>\n+ <param name="tumor" ftype="bam" value="tumor.bam" />\n+ <param name="normal" ftype="bam" value="normal.bam" />\n+ </conditional>\n+ <param name="reference_sequence" ftype="fasta" value="chr20.fa" />\n+ <param name="gzipped_output" value="false" />\n+ <param name="reference_source_selector" value="history" />\n+ <param name="optional_parameters" value="no" />\n+ <param name="advanced_parameters" value="no" />\n+ <param name="output_parameters" value="no" />\n+ <output name="output_vcf" file="Mutect2-out6.vcf" lines_diff="2" />\n+ </test>\n </tests>\n <help><![CDATA[Call somatic short variants via local assembly of haplotypes. Short\n variants include single nucleotide (SNV) and insertion and deletion\n' |
| b |
| diff -r 3be27a9a7313 -r 287c4af133e6 macros.xml --- a/macros.xml Fri Apr 10 14:10:55 2020 -0400 +++ b/macros.xml Sun May 10 17:58:00 2020 -0400 |
| [ |
| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> - <token name="@VERSION@">4.1.4.0</token> - <token name="@WRAPPER_VERSION@">@VERSION@+galaxy</token> + <token name="@VERSION@">4.1.7.0</token> + <token name="@WRAPPER_VERSION@">@VERSION@+galaxy0</token> <xml name="requirements"> <requirements> @@ -290,45 +290,58 @@ </xml> <!--BAM input--> - <template name="picard_bam_input"> - --INPUT input.bam - </template> - - <template name="gatk_bam_input"> - --input input.bam + <template name="picard_tumor_bam_input"> + --INPUT tumor.bam </template> - <template name="bam_index_pre_chth"><![CDATA[ + <template name="gatk_tumor_bam_input"> + --input tumor.bam + </template> + + <template name="tumor_bam_index_pre_chth"><![CDATA[ #for $sect in $sections - #if $varExists($sect + "input") - #if $getVar($sect + "input").is_of_type("bam") - ln -s $getVar($sect + "input") input.bam && - samtools index input.bam && - #else - ln -s $getVar($sect + "input") input.sam && - samtools view -bS input.sam -o input.bam && - samtools index input.bam && - #end if + #if $varExists($sect + "tumor") + ln -s $getVar($sect + "tumor") tumor.bam && + ln -s '${tumor.metadata.bam_index}' tumor.bam.bai && #end if #end for ]]></template> - <xml name="gatk_bam_req_params"> - <param argument="--input" type="data" format="bam,sam" label="Input BAM/SAM/CRAM file" /> + <xml name="gatk_tumor_bam_req_params"> + <param name="tumor" argument="--tumor" type="data" format="bam" label="Input Tumor BAM file" /> </xml> - <template name="picard_bam_index"><![CDATA[ - #if $input.is_of_type("bam") - ln -s $INPUT input.bam && - samtools index input.bam && - #else - ln -s $INPUT input.sam && - samtools view -bS input.sam -o input.bam && - samtools index input.bam && - #end if + <template name="picard_tumor_bam_index"><![CDATA[ + ln -s $INPUT tumor.bam && + ln -s $INPUT tumor.bam.bai && ]]></template> + <template name="picard_normal_bam_input"> + --INPUT normal.bam + </template> + <template name="gatk_normal_bam_input"> + --input normal.bam + </template> + + <template name="normal_bam_index_pre_chth"><![CDATA[ + #for $sect in $sections + #if $varExists($sect + "normal") + ln -s $getVar($sect + "normal") normal.bam && + ln -s '${normal.metadata.bam_index}' normal.bam.bai && + #end if + #end for + ]]></template> + + <xml name="gatk_normal_bam_req_params"> + <param name="normal" argument="--normal" type="data" format="bam" label="Input Normal BAM file" /> + </xml> + + <template name="picard_normal_bam_index"><![CDATA[ + ln -s $INPUT normal.bam && + ln -s $INPUT normal.bam.bai && + ]]></template> + <!--Output goes to stdout, no output parameter exists.--> <template name="stdout_to_output"> > output.txt |
| b |
| diff -r 3be27a9a7313 -r 287c4af133e6 test-data/Mutect2-out1.vcf --- a/test-data/Mutect2-out1.vcf Fri Apr 10 14:10:55 2020 -0400 +++ b/test-data/Mutect2-out1.vcf Sun May 10 17:58:00 2020 -0400 |
| b |
| b'@@ -6,12 +6,14 @@\n ##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele">\n ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n-##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">\n+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozygous and is not intended to describe called alleles">\n ##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">\n ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">\n ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)">\n ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher\'s Exact Test to detect strand bias.">\n-##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample SRR8525881 --output output.vcf --input input.bam --reference reference.fa --QUIET true --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --dont-trim-active-regions false --max-extension 25 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --min-base-quality-score 10 --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active 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 --cl'..b'6\t.\tC\tT\t.\t.\tAS_SB_TABLE=22,34|6,6;DP=68;ECNT=21;MBQ=37,37;MFRL=270,305;MMQ=60,60;MPOS=47;POPAF=7.30;TLOD=37.06\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:56,12:0.197:68:20,5:33,4:22,34,6,6\n+K03455\t4418\t.\tA\tG\t.\t.\tAS_SB_TABLE=26,38|1,2;DP=67;ECNT=21;MBQ=37,37;MFRL=284,229;MMQ=60,60;MPOS=45;POPAF=7.30;TLOD=6.77\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:64,3:0.062:67:24,3:35,0:26,38,1,2\n+K03455\t4421\t.\tT\tC\t.\t.\tAS_SB_TABLE=11,20|16,20;DP=67;ECNT=21;MBQ=34,38;MFRL=263,291;MMQ=60,60;MPOS=35;POPAF=7.30;TLOD=142.09\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:31,36:0.538:67:16,14:12,21:11,20,16,20\n+K03455\t4424\t.\tT\tC\t.\t.\tAS_SB_TABLE=13,24|13,15;DP=65;ECNT=21;MBQ=37,38;MFRL=254,295;MMQ=60,60;MPOS=35;POPAF=7.30;TLOD=102.79\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:37,28:0.444:65:15,9:15,17:13,24,13,15\n+K03455\t4430\t.\tT\tC\t.\t.\tAS_SB_TABLE=25,37|1,2;DP=65;ECNT=21;MBQ=37,36;MFRL=280,300;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=7.02\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:62,3:0.063:65:26,2:32,1:25,37,1,2\n+K03455\t4439\t.\tA\tG\t.\t.\tAS_SB_TABLE=22,31|3,4;DP=60;ECNT=21;MBQ=38,35;MFRL=287,210;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=21.26\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:53,7:0.121:60:23,3:26,4:22,31,3,4\n+K03455\t4442\t.\tAG\tGA\t.\t.\tAS_SB_TABLE=21,30|3,4;DP=59;ECNT=21;MBQ=37,33;MFRL=287,209;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=18.12\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:51,7:0.142:58:20,2:25,5:21,30,3,4\n+K03455\t4443\t.\tG\tA\t.\t.\tAS_SB_TABLE=12,19|11,12;DP=59;ECNT=21;MBQ=35,38;MFRL=276,291;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=78.51\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:31,23:0.421:54:14,10:13,10:12,19,11,12\n+K03455\t4448\t.\tC\tA\t.\t.\tAS_SB_TABLE=22,31|1,2;DP=57;ECNT=21;MBQ=37,20;MFRL=287,126;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=8.91\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:53,3:0.055:56:21,0:27,2:22,31,1,2\n+K03455\t4449\t.\tC\tT\t.\t.\tAS_SB_TABLE=13,16|11,15;DP=55;ECNT=21;MBQ=37,38;MFRL=209,322;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=97.76\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:29,26:0.491:55:11,12:16,13:13,16,11,15\n+K03455\t4460\t.\tT\tC\t.\t.\tAS_SB_TABLE=22,22|2,5;DP=51;ECNT=21;MBQ=37,37;MFRL=279,321;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=22.02\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:44,7:0.163:51:17,3:24,3:22,22,2,5\n+K03455\t4465\t.\tT\tTGGCC\t.\t.\tAS_SB_TABLE=19,20|4,4;DP=50;ECNT=21;MBQ=37,35;MFRL=290,176;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=26.66\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:39,8:0.155:47:14,6:22,1:19,20,4,4\n+K03455\t4466\t.\tA\tG,AGTG\t.\t.\tAS_SB_TABLE=16,17|2,3|4,4;DP=49;ECNT=21;MBQ=37,38,37;MFRL=310,207,176;MMQ=60,60,60;MPOS=20,25;POPAF=7.30,7.30;TLOD=15.50,28.09\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1/2:33,5,8:0.154,0.179:46:12,1,6:16,4,1:16,17,6,7\n+K03455\t4478\t.\tT\tC\t.\t.\tAS_SB_TABLE=12,13|5,6;DP=36;ECNT=21;MBQ=37,32;MFRL=323,205;MMQ=60,60;MPOS=10;POPAF=7.30;TLOD=44.55\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:25,11:0.306:36:9,6:15,4:12,13,5,6\n+K03455\t4505\t.\tA\tG\t.\t.\tAS_SB_TABLE=2,1|11,6;DP=20;ECNT=21;MBQ=39,37;MFRL=394,323;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=72.12\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:3,17:0.818:20:2,6:1,8:2,1,11,6\n+K03455\t4508\t.\tA\tT\t.\t.\tAS_SB_TABLE=2,3|10,3;DP=18;ECNT=21;MBQ=39,35;MFRL=287,335;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=52.71\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:5,13:0.700:18:3,5:2,8:2,3,10,3\n+K03455\t4511\t.\tG\tA\t.\t.\tAS_SB_TABLE=2,1|10,5;DP=18;ECNT=21;MBQ=37,35;MFRL=394,323;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=62.74\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:3,15:0.800:18:2,5:1,7:2,1,10,5\n+K03455\t4526\t.\tT\tC\t.\t.\tAS_SB_TABLE=0,0|11,2;DP=13;ECNT=21;MBQ=0,36;MFRL=0,323;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=57.35\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:0,13:0.933:13:0,7:0,6:0,0,11,2\n+K03455\t4528\t.\tT\tTCA\t.\t.\tAS_SB_TABLE=10,1|1,1;DP=13;ECNT=21;MBQ=38,37;MFRL=323,421;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=5.52\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:11,2:0.200:13:5,1:4,1:0|1:4528_T_TCA:4528:10,1,1,1\n+K03455\t4530\t.\tCTT\tC\t.\t.\tAS_SB_TABLE=9,1|1,1;DP=13;ECNT=21;MBQ=35,38;MFRL=323,421;MMQ=60,60;MPOS=34;POPAF=7.30;RPA=4,2;RU=T;STR;TLOD=6.12\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:10,2:0.213:12:5,1:4,1:0|1:4528_T_TCA:4528:9,1,1,1\n+K03455\t4532\t.\tT\tC\t.\t.\tAS_SB_TABLE=0,0|11,0;DP=13;ECNT=21;MBQ=0,27;MFRL=0,323;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=39.42\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:0,11:0.926:11:0,6:0,2:0,0,11,0\n' |
| b |
| diff -r 3be27a9a7313 -r 287c4af133e6 test-data/Mutect2-out2.vcf --- a/test-data/Mutect2-out2.vcf Fri Apr 10 14:10:55 2020 -0400 +++ b/test-data/Mutect2-out2.vcf Sun May 10 17:58:00 2020 -0400 |
| b |
| b'@@ -6,12 +6,14 @@\n ##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele">\n ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n-##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">\n+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozygous and is not intended to describe called alleles">\n ##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">\n ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">\n ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)">\n ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher\'s Exact Test to detect strand bias.">\n-##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample SRR8525881 --output output.vcf --input input.bam --reference reference.fa --QUIET true --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --dont-trim-active-regions false --max-extension 25 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --min-base-quality-score 10 --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active 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 --cl'..b'POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1\n+K03455\t7455\t.\tA\tATG\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=95;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1\n+K03455\t7457\t.\tTGA\tT\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=99;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1\n+K03455\t7460\t.\tCA\tC\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,37;MFRL=0,486;MMQ=60,60;MPOS=100;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1\n+K03455\t7468\t.\tCC\tTA\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=107;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,2\n+K03455\t7478\t.\tC\tT\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=117;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2\n+K03455\t7491\t.\tA\tT\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=118;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2\n+K03455\t7494\t.\tA\tG\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=115;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2\n+K03455\t7508\t.\tGA\tAG\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=101;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2\n+K03455\t7541\t.\tC\tCGA\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=68;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2\n+K03455\t7542\t.\tAGT\tA\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=65;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2\n+K03455\t7548\t.\tC\tA\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=61;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2\n+K03455\t7555\t.\tGA\tAT\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=54;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2\n+K03455\t7560\t.\tTC\tGT\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,38;MFRL=0,586;MMQ=60,50;MPOS=49;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2\n+K03455\t7568\t.\tT\tC\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=41;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2\n+K03455\t7571\t.\tT\tC\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=38;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2\n+K03455\t7581\t.\tC\tA\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=28;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2\n+K03455\t7584\t.\tT\tC\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=25;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2\n+K03455\t7603\t.\tA\tAGGG\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,37;MFRL=0,586;MMQ=60,50;MPOS=6;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2\n+K03455\t7604\t.\tT\tG\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,33;MFRL=0,586;MMQ=60,50;MPOS=2;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,1:0|1:7541_C_CGA:7541:0,0,0,2\n' |
| b |
| diff -r 3be27a9a7313 -r 287c4af133e6 test-data/Mutect2-out3.vcf --- a/test-data/Mutect2-out3.vcf Fri Apr 10 14:10:55 2020 -0400 +++ b/test-data/Mutect2-out3.vcf Sun May 10 17:58:00 2020 -0400 |
| b |
| b'@@ -6,12 +6,14 @@\n ##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele">\n ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n-##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">\n+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozygous and is not intended to describe called alleles">\n ##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">\n ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">\n ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)">\n ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher\'s Exact Test to detect strand bias.">\n-##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --tumor-sample SRR8525881 --af-of-alleles-not-in-resource -1.0 --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --normal-lod 2.2 --base-quality-score-threshold 18 --native-pair-hmm-threads 1 --min-base-quality-score 10 --output output.vcf --max-reads-per-alignment-start 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --input input.bam --read-validation-stringency SILENT --reference reference.fa --add-output-sam-program-record true --add-output-vcf-command-line true --verbosity ERROR --QUIET true --gcs-max-retries 20 --annotation StrandBiasBySample --annotation BaseQualityHistogram --annotation OrientationBiasReadCounts --annotation-group StandardMutectAnnotation --genotype-pon-sites false --genotype-germline-sites false --mitochondria-mode false --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --dont-trim-active-regions false --max-extension 25 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --seconds-between-progress-updates 10.0 --disable'..b'0,32;MFRL=245,276;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=3.17\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:581,8:0.012:589:285,2:265,5:314,267,4,4\n+K03455\t2872\t.\tT\tA\t.\t.\tAS_SB_TABLE=267,300|25,0;BQHIST=14,1,2,15,2,0,16,0,11,17,6,6,18,15,51,19,0,38,20,0,167,27,1,1,29,0,16,30,0,3,31,0,9,32,0,22,33,0,29,34,0,12,35,0,12,36,0,9,37,0,78,38,0,48,39,0,53;DP=628;ECNT=12;MBQ=29,18;MFRL=240,283;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=3.43\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:567,25:0.023:592:225,1:234,0:267,300,25,0\n+K03455\t2874\t.\tC\tT\t.\t.\tAS_SB_TABLE=1,0|300,303;BQHIST=16,0,6,17,1,5,18,0,54,19,0,13,20,0,199,29,0,4,30,0,2,31,0,11,32,0,32,33,0,41,34,0,13,35,0,13,36,0,11,37,0,87,38,0,54,39,0,51;DP=606;ECNT=12;MBQ=17,32;MFRL=360,241;MMQ=60,60;MPOS=33;POPAF=7.30;TLOD=2043.53\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:1,603:0.997:604:0,265:0,253:1,0,300,303\n+K03455\t2882\t.\tG\tT\t.\t.\tAS_SB_TABLE=1,0|295,283;BQHIST=14,2,0,16,6,0,17,6,0,18,21,0,19,12,0,20,195,0,29,2,0,30,4,0,31,4,1,32,3,0,33,25,0,34,1,0,35,21,0,36,11,0,37,85,0,38,52,0,39,112,0;DP=579;ECNT=12;MBQ=31,35;MFRL=360,246;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=1927.63\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:1,578:0.997:579:1,259:0,256:1,0,295,283\n+K03455\t2889\t.\tG\tA\t.\t.\tAS_SB_TABLE=289,272|7,1;BQHIST=14,0,11,15,0,1,16,0,4,17,0,5,18,0,13,19,0,17,20,0,190,29,1,1,30,0,3,31,0,1,32,0,7,33,2,31,34,1,4,35,0,9,36,0,15,37,1,79,38,1,72,39,2,95,40,0,1;DP=580;ECNT=12;MBQ=33,36;MFRL=249,291;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=9.57\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:561,8:0.018:569:248,4:260,4:289,272,7,1\n+K03455\t2891\t.\tA\tG\t.\t.\tAS_SB_TABLE=286,269|5,4;BQHIST=14,0,1,16,6,0,17,9,0,18,18,0,19,8,0,20,179,6,30,1,0,31,4,0,32,8,0,33,25,1,34,2,0,35,26,0,36,7,1,37,78,0,38,85,0,39,89,0;DP=576;ECNT=12;MBQ=35,20;MFRL=249,231;MMQ=60,60;MPOS=45;POPAF=7.30;TLOD=8.78\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:555,9:0.013:564:243,4:261,4:286,269,5,4\n+K03455\t2894\t.\tT\tC\t.\t.\tAS_SB_TABLE=0,0|291,273;BQHIST=14,1,0,15,5,0,16,4,0,17,13,0,18,33,0,19,4,0,20,162,0,27,1,0,29,3,0,30,5,0,31,1,0,32,6,0,33,25,0,34,12,0,35,5,0,36,8,0,37,83,0,38,69,0,39,116,0;DP=564;ECNT=12;MBQ=0,35;MFRL=0,250;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=1813.95\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:0,564:0.998:564:0,243:0,253:0,0,291,273\n+K03455\t2906\t.\tC\tT\t.\t.\tAS_SB_TABLE=0,0|246,262;BQHIST=16,0,2,18,0,4,19,0,10,20,0,145,30,0,2,31,0,2,32,0,3,33,0,21,34,0,3,35,0,19,36,0,11,37,0,61,38,0,79,39,0,146;DP=508;ECNT=12;MBQ=0,37;MFRL=0,251;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=2411.23\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,508:0.998:508:0,232:0,260:0|1:2906_C_T:2906:0,0,246,262\n+K03455\t2913\t.\tG\tA\t.\t.\tAS_SB_TABLE=0,0|245,260;BQHIST=18,5,0,19,5,0,20,134,0,29,1,0,30,2,0,31,2,0,32,2,0,33,17,0,34,1,0,35,6,0,36,2,0,37,64,0,38,68,0,39,184,0,40,4,0;DP=505;ECNT=12;MBQ=0,38;MFRL=0,251;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=2402.33\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,505:0.998:505:0,230:0,257:0|1:2906_C_T:2906:0,0,245,260\n+K03455\t2987\t.\tC\tT\t.\t.\tAS_SB_TABLE=0,0|86,133;BQHIST=16,0,3,17,0,3,19,0,11,20,0,15,30,0,2,31,0,9,32,0,7,33,0,31,34,0,8,35,0,9,36,0,1,37,0,47,38,0,34,39,0,39;DP=223;ECNT=4;MBQ=0,37;MFRL=0,264;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=847.13\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:0,219:0.995:219:0,99:0,103:0,0,86,133\n+K03455\t2992\t.\tT\tG\t.\t.\tAS_SB_TABLE=74,105|9,0;BQHIST=16,1,0,17,3,0,18,1,7,19,23,0,20,13,1,29,1,0,31,8,0,32,8,0,33,18,1,34,9,0,35,4,0,36,4,0,37,35,0,38,30,0,39,21,0;DP=206;ECNT=4;MBQ=36,18;MFRL=271,260;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=3.85\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:179,9:0.043:188:74,2:77,0:74,105,9,0\n+K03455\t3016\t.\tC\tA\t.\t.\tAS_SB_TABLE=61,27|7,0;BQHIST=14,0,2,15,0,2,18,6,26,29,0,1,30,0,3,32,0,5,33,1,12,34,0,2,35,0,2,36,0,8,37,0,5,38,0,16,39,0,4;DP=100;ECNT=4;MBQ=33,18;MFRL=276,255;MMQ=60,60;MPOS=5;POPAF=7.30;TLOD=5.62\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:88,7:0.081:95:24,1:34,0:61,27,7,0\n+K03455\t3020\t.\tA\tG\t.\t.\tAS_SB_TABLE=0,0|65,25;BQHIST=14,0,12,16,0,1,18,0,1,27,0,3,29,0,3,30,0,8,32,0,8,33,0,2,34,0,1,35,0,1,36,0,21,37,0,4,38,0,23,39,0,1;DP=95;ECNT=4;MBQ=0,36;MFRL=0,284;MMQ=60,60;MPOS=7;POPAF=7.30;TLOD=324.41\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:0,90:0.989:90:0,32:0,43:0,0,65,25\n' |
| b |
| diff -r 3be27a9a7313 -r 287c4af133e6 test-data/Mutect2-out4.vcf --- a/test-data/Mutect2-out4.vcf Fri Apr 10 14:10:55 2020 -0400 +++ b/test-data/Mutect2-out4.vcf Sun May 10 17:58:00 2020 -0400 |
| b |
| b'@@ -6,12 +6,14 @@\n ##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele">\n ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n-##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">\n+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozygous and is not intended to describe called alleles">\n ##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">\n ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">\n ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)">\n ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher\'s Exact Test to detect strand bias.">\n-##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --tumor-sample SRR8525881 --af-of-alleles-not-in-resource -1.0 --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --minimum-allele-fraction 0.0 --dont-trim-active-regions true --num-pruning-samples 1 --min-dangling-branch-length 4 --max-num-haplotypes-in-population 128 --min-pruning 2 --pruning-lod-threshold 2.30258509299 --max-unpruned-variants 100 --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 1 --bam-writer-type CALLED_HAPLOTYPES --min-base-quality-score 10 --smith-waterman FASTEST_AVAILABLE --emit-ref-confidence NONE --max-mnp-distance 1 --output output.vcf --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --input input.bam --read-validation-stringency SILENT --reference reference.fa --add-output-sam-program-record true --add-output-vcf-command-line true --verbosity ERROR --QUIET true --gcs-max-retries 20 --genotype-pon-sites false --genotype-germline-sites false --mitochondria-mode false --callable-depth 10 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --independent-mates false --disable-adaptive-pruning false --max-extension 25 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --recover-all-dangling-branches false --adaptive-pruning-initial-error-rate 0.001 --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --native-pair-hmm-use-double-precision false --dont-use-soft-clipped-bases false --force-call-filtered-alleles false --force-active false --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 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|
| b |
| diff -r 3be27a9a7313 -r 287c4af133e6 test-data/Mutect2-out5-1.tabular --- a/test-data/Mutect2-out5-1.tabular Fri Apr 10 14:10:55 2020 -0400 +++ b/test-data/Mutect2-out5-1.tabular Sun May 10 17:58:00 2020 -0400 |
| b |
| b'@@ -1,9721 +1,70 @@\n #track 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\t9681\t9682\tstate\t0.00000\n-K03455\t9682\t9683\tstate\t0.00000\n-K03455\t9683\t9684\tstate\t0.00000\n-K03455\t9684\t9685\tstate\t0.00000\n-K03455\t9685\t9686\tstate\t0.00000\n-K03455\t9686\t9687\tstate\t0.00000\n-K03455\t9687\t9688\tstate\t0.00000\n-K03455\t9688\t9689\tstate\t0.00000\n-K03455\t9689\t9690\tstate\t0.00000\n-K03455\t9690\t9691\tstate\t0.00000\n-K03455\t9691\t9692\tstate\t0.00000\n-K03455\t9692\t9693\tstate\t0.00000\n-K03455\t9693\t9694\tstate\t0.00000\n-K03455\t9694\t9695\tstate\t0.00000\n-K03455\t9695\t9696\tstate\t0.00000\n-K03455\t9696\t9697\tstate\t0.00000\n-K03455\t9697\t9698\tstate\t0.00000\n-K03455\t9698\t9699\tstate\t0.00000\n-K03455\t9699\t9700\tstate\t0.00000\n-K03455\t9700\t9701\tstate\t0.00000\n-K03455\t9701\t9702\tstate\t0.00000\n-K03455\t9702\t9703\tstate\t0.00000\n-K03455\t9703\t9704\tstate\t0.00000\n-K03455\t9704\t9705\tstate\t0.00000\n-K03455\t9705\t9706\tstate\t0.00000\n-K03455\t9706\t9707\tstate\t0.00000\n-K03455\t9707\t9708\tstate\t0.00000\n-K03455\t9708\t9709\tstate\t0.00000\n-K03455\t9709\t9710\tstate\t0.00000\n-K03455\t9710\t9711\tstate\t0.00000\n-K03455\t9711\t9712\tstate\t0.00000\n-K03455\t9712\t9713\tstate\t0.00000\n-K03455\t9713\t9714\tstate\t0.00000\n-K03455\t9714\t9715\tstate\t0.00000\n-K03455\t9715\t9716\tstate\t0.00000\n-K03455\t9716\t9717\tstate\t0.00000\n-K03455\t9717\t9718\tstate\t0.00000\n-K03455\t9718\t9719\tstate\t0.00000\n+Chromosome\tStart\tEnd\tFeature\tAssemblyRegions\n+K03455\t0\t1\tend-marker\t0.00000\n+K03455\t0\t300\tsize=300\t-1.00000\n+K03455\t300\t301\tend-marker\t0.00000\n+K03455\t300\t600\tsize=300\t-1.00000\n+K03455\t600\t601\tend-marker\t0.00000\n+K03455\t600\t900\tsize=300\t-1.00000\n+K03455\t900\t901\tend-marker\t0.00000\n+K03455\t900\t1200\tsize=300\t-1.00000\n+K03455\t1200\t1201\tend-marker\t0.00000\n+K03455\t1200\t1500\tsize=300\t-1.00000\n+K03455\t1500\t1501\tend-marker\t0.00000\n+K03455\t1500\t1800\tsize=300\t-1.00000\n+K03455\t1800\t1801\tend-marker\t0.00000\n+K03455\t1800\t2057\tsize=257\t-1.00000\n+K03455\t2057\t2058\tend-marker\t0.00000\n+K03455\t2057\t2342\tsize=285\t1.00000\n+K03455\t2342\t2343\tend-marker\t0.00000\n+K03455\t2342\t2481\tsize=139\t1.00000\n+K03455\t2481\t2482\tend-marker\t0.00000\n+K03455\t2481\t2781\tsize=300\t-1.00000\n+K03455\t2781\t2782\tend-marker\t0.00000\n+K03455\t2781\t3081\tsize=300\t-1.00000\n+K03455\t3081\t3082\tend-marker\t0.00000\n+K03455\t3081\t3381\tsize=300\t-1.00000\n+K03455\t3381\t3382\tend-marker\t0.00000\n+K03455\t3381\t3681\tsize=300\t-1.00000\n+K03455\t3681\t3682\tend-marker\t0.00000\n+K03455\t3681\t3981\tsize=300\t-1.00000\n+K03455\t3981\t3982\tend-marker\t0.00000\n+K03455\t3981\t4281\tsize=300\t-1.00000\n+K03455\t4281\t4282\tend-marker\t0.00000\n+K03455\t4281\t4581\tsize=300\t-1.00000\n+K03455\t4581\t4582\tend-marker\t0.00000\n+K03455\t4581\t4881\tsize=300\t-1.00000\n+K03455\t4881\t4882\tend-marker\t0.00000\n+K03455\t4881\t5181\tsize=300\t-1.00000\n+K03455\t5181\t5182\tend-marker\t0.00000\n+K03455\t5181\t5481\tsize=300\t-1.00000\n+K03455\t5481\t5482\tend-marker\t0.00000\n+K03455\t5481\t5781\tsize=300\t-1.00000\n+K03455\t5781\t5782\tend-marker\t0.00000\n+K03455\t5781\t6081\tsize=300\t-1.00000\n+K03455\t6081\t6082\tend-marker\t0.00000\n+K03455\t6081\t6381\tsize=300\t-1.00000\n+K03455\t6381\t6382\tend-marker\t0.00000\n+K03455\t6381\t6681\tsize=300\t-1.00000\n+K03455\t6681\t6682\tend-marker\t0.00000\n+K03455\t6681\t6981\tsize=300\t-1.00000\n+K03455\t6981\t6982\tend-marker\t0.00000\n+K03455\t6981\t7281\tsize=300\t-1.00000\n+K03455\t7281\t7282\tend-marker\t0.00000\n+K03455\t7281\t7581\tsize=300\t-1.00000\n+K03455\t7581\t7582\tend-marker\t0.00000\n+K03455\t7581\t7881\tsize=300\t-1.00000\n+K03455\t7881\t7882\tend-marker\t0.00000\n+K03455\t7881\t8181\tsize=300\t-1.00000\n+K03455\t8181\t8182\tend-marker\t0.00000\n+K03455\t8181\t8481\tsize=300\t-1.00000\n+K03455\t8481\t8482\tend-marker\t0.00000\n+K03455\t8481\t8781\tsize=300\t-1.00000\n+K03455\t8781\t8782\tend-marker\t0.00000\n+K03455\t8781\t9081\tsize=300\t-1.00000\n+K03455\t9081\t9082\tend-marker\t0.00000\n+K03455\t9081\t9381\tsize=300\t-1.00000\n+K03455\t9381\t9382\tend-marker\t0.00000\n+K03455\t9381\t9681\tsize=300\t-1.00000\n+K03455\t9681\t9682\tend-marker\t0.00000\n+K03455\t9681\t9719\tsize=38\t-1.00000\n' |
| b |
| diff -r 3be27a9a7313 -r 287c4af133e6 test-data/Mutect2-out5-2.tabular --- a/test-data/Mutect2-out5-2.tabular Fri Apr 10 14:10:55 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,70 +0,0 @@ -#track graphType=line -Chromosome Start End Feature AssemblyRegions -K03455 0 1 end-marker 0.00000 -K03455 0 300 size=300 -1.00000 -K03455 300 301 end-marker 0.00000 -K03455 300 600 size=300 -1.00000 -K03455 600 601 end-marker 0.00000 -K03455 600 900 size=300 -1.00000 -K03455 900 901 end-marker 0.00000 -K03455 900 1200 size=300 -1.00000 -K03455 1200 1201 end-marker 0.00000 -K03455 1200 1500 size=300 -1.00000 -K03455 1500 1501 end-marker 0.00000 -K03455 1500 1800 size=300 -1.00000 -K03455 1800 1801 end-marker 0.00000 -K03455 1800 2057 size=257 -1.00000 -K03455 2057 2058 end-marker 0.00000 -K03455 2057 2342 size=285 1.00000 -K03455 2342 2343 end-marker 0.00000 -K03455 2342 2481 size=139 1.00000 -K03455 2481 2482 end-marker 0.00000 -K03455 2481 2781 size=300 -1.00000 -K03455 2781 2782 end-marker 0.00000 -K03455 2781 3081 size=300 -1.00000 -K03455 3081 3082 end-marker 0.00000 -K03455 3081 3381 size=300 -1.00000 -K03455 3381 3382 end-marker 0.00000 -K03455 3381 3681 size=300 -1.00000 -K03455 3681 3682 end-marker 0.00000 -K03455 3681 3981 size=300 -1.00000 -K03455 3981 3982 end-marker 0.00000 -K03455 3981 4281 size=300 -1.00000 -K03455 4281 4282 end-marker 0.00000 -K03455 4281 4581 size=300 -1.00000 -K03455 4581 4582 end-marker 0.00000 -K03455 4581 4881 size=300 -1.00000 -K03455 4881 4882 end-marker 0.00000 -K03455 4881 5181 size=300 -1.00000 -K03455 5181 5182 end-marker 0.00000 -K03455 5181 5481 size=300 -1.00000 -K03455 5481 5482 end-marker 0.00000 -K03455 5481 5781 size=300 -1.00000 -K03455 5781 5782 end-marker 0.00000 -K03455 5781 6081 size=300 -1.00000 -K03455 6081 6082 end-marker 0.00000 -K03455 6081 6381 size=300 -1.00000 -K03455 6381 6382 end-marker 0.00000 -K03455 6381 6681 size=300 -1.00000 -K03455 6681 6682 end-marker 0.00000 -K03455 6681 6981 size=300 -1.00000 -K03455 6981 6982 end-marker 0.00000 -K03455 6981 7281 size=300 -1.00000 -K03455 7281 7282 end-marker 0.00000 -K03455 7281 7581 size=300 -1.00000 -K03455 7581 7582 end-marker 0.00000 -K03455 7581 7881 size=300 -1.00000 -K03455 7881 7882 end-marker 0.00000 -K03455 7881 8181 size=300 -1.00000 -K03455 8181 8182 end-marker 0.00000 -K03455 8181 8481 size=300 -1.00000 -K03455 8481 8482 end-marker 0.00000 -K03455 8481 8781 size=300 -1.00000 -K03455 8781 8782 end-marker 0.00000 -K03455 8781 9081 size=300 -1.00000 -K03455 9081 9082 end-marker 0.00000 -K03455 9081 9381 size=300 -1.00000 -K03455 9381 9382 end-marker 0.00000 -K03455 9381 9681 size=300 -1.00000 -K03455 9681 9682 end-marker 0.00000 -K03455 9681 9719 size=38 -1.00000 |
| b |
| diff -r 3be27a9a7313 -r 287c4af133e6 test-data/Mutect2-out5.bam |
| b |
| Binary file test-data/Mutect2-out5.bam has changed |
| b |
| diff -r 3be27a9a7313 -r 287c4af133e6 test-data/Mutect2-out5.vcf --- a/test-data/Mutect2-out5.vcf Fri Apr 10 14:10:55 2020 -0400 +++ b/test-data/Mutect2-out5.vcf Sun May 10 17:58:00 2020 -0400 |
| b |
| b'@@ -6,12 +6,14 @@\n ##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele">\n ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n-##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">\n+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozygous and is not intended to describe called alleles">\n ##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">\n ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">\n ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)">\n ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher\'s Exact Test to detect strand bias.">\n-##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample SRR8525881 --bam-output debug.bam --output output.vcf --activity-profile-out activity-profile.tab --assembly-region-out assembly-region.tab --input input.bam --reference reference.fa --QUIET true --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --dont-trim-active-regions false --max-extension 25 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --min-base-quality-score 10 --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active 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-v'..b'PAF=7.30;TLOD=12.44\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:39,5:0.098:44:23,2:16,3:0|1:2200_ACTC_A:2200:27,12,3,2\n+K03455\t2258\t.\tGG\tAA\t.\t.\tAS_SB_TABLE=6,0|26,14;DP=46;ECNT=41;MBQ=39,39;MFRL=216,239;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=159.02\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:6,40:0.859:46:3,22:3,17:0|1:2258_GG_AA:2258:6,0,26,14\n+K03455\t2259\t.\tG\tA\t.\t.\tAS_SB_TABLE=0,0|10,3;DP=46;ECNT=41;MBQ=0,37;MFRL=0,241;MMQ=60,60;MPOS=39;POPAF=7.30;TLOD=13.48\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t1|0:0,13:0.961:13:0,5:0,8:1|0:2258_GG_AA:2258:0,0,10,3\n+K03455\t2282\t.\tC\tT\t.\t.\tAS_SB_TABLE=32,24|2,2;DP=60;ECNT=41;MBQ=36,20;MFRL=239,182;MMQ=60,60;MPOS=44;POPAF=7.30;TLOD=9.01\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:56,4:0.059:60:24,1:24,2:32,24,2,2\n+K03455\t2285\t.\tC\tT\t.\t.\tAS_SB_TABLE=30,23|6,3;DP=62;ECNT=41;MBQ=29,38;MFRL=236,205;MMQ=60,60;MPOS=49;POPAF=7.30;TLOD=26.48\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:53,9:0.151:62:24,3:21,4:30,23,6,3\n+K03455\t2287\t.\tCA\tAT\t.\t.\tAS_SB_TABLE=32,26|4,3;DP=65;ECNT=41;MBQ=33,37;MFRL=234,285;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=17.41\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:58,7:0.133:65:25,1:24,2:32,26,4,3\n+K03455\t2300\t.\tG\tA\t.\t.\tAS_SB_TABLE=6,6|26,23;DP=63;ECNT=41;MBQ=31,32;MFRL=229,236;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=211.84\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:12,49:0.796:61:3,20:5,22:6,6,26,23\n+K03455\t2303\t.\tGCA\tG\t.\t.\tAS_SB_TABLE=7,8|25,20;DP=61;ECNT=41;MBQ=36,31;MFRL=225,241;MMQ=60,60;MPOS=40;POPAF=7.30;TLOD=171.69\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:15,45:0.735:60:2,18:9,20:7,8,25,20\n+K03455\t2304\t.\tCAA\tGTG\t.\t.\tAS_SB_TABLE=6,6|10,9;DP=61;ECNT=41;MBQ=33,20;MFRL=229,235;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=3.47\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:12,19:0.531:31:4,0:7,3:6,6,10,9\n+K03455\t2306\t.\tA\tATG,G\t.\t.\tAS_SB_TABLE=2,2|26,22|4,4;DP=60;ECNT=41;MBQ=29,32,33;MFRL=182,239,280;MMQ=60,60,60;MPOS=39,19;POPAF=7.30,7.30;TLOD=175.97,22.08\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1/2:4,48,8:0.779,0.164:60:2,20,2:2,23,4:2,2,30,26\n+K03455\t2315\t.\tA\tG\t.\t.\tAS_SB_TABLE=19,19|11,9;DP=59;ECNT=41;MBQ=37,38;MFRL=229,244;MMQ=60,60;MPOS=51;POPAF=7.30;TLOD=74.64\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:38,20:0.379:58:17,6:15,14:0|1:2315_A_G:2315:19,19,11,9\n+K03455\t2321\t.\tA\tC\t.\t.\tAS_SB_TABLE=17,19|11,9;DP=56;ECNT=41;MBQ=34,37;MFRL=229,244;MMQ=60,60;MPOS=49;POPAF=7.30;TLOD=75.24\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:36,20:0.392:56:16,6:17,14:0|1:2315_A_G:2315:17,19,11,9\n+K03455\t2349\t.\tT\tC\t.\t.\tAS_SB_TABLE=23,24|4,5;DP=56;ECNT=9;MBQ=35,35;MFRL=235,285;MMQ=60,60;MPOS=54;POPAF=7.30;TLOD=28.30\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:47,9:0.190:56:19,3:22,5:23,24,4,5\n+K03455\t2360\t.\tG\tA\t.\t.\tAS_SB_TABLE=19,20|4,6;DP=49;ECNT=9;MBQ=37,27;MFRL=235,272;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=28.07\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:39,10:0.229:49:15,3:22,3:19,20,4,6\n+K03455\t2362\t.\tG\tA\t.\t.\tAS_SB_TABLE=0,0|21,26;DP=49;ECNT=9;MBQ=0,36;MFRL=0,241;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=181.58\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:0,47:0.978:47:0,19:0,25:0,0,21,26\n+K03455\t2372\t.\tA\tG\t.\t.\tAS_SB_TABLE=16,19|4,5;DP=44;ECNT=9;MBQ=37,36;MFRL=241,259;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=30.36\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:35,9:0.234:44:9,3:17,5:16,19,4,5\n+K03455\t2374\t.\tG\tA\t.\t.\tAS_SB_TABLE=12,22|2,2;DP=38;ECNT=9;MBQ=37,35;MFRL=234,284;MMQ=60,60;MPOS=7;POPAF=7.30;TLOD=7.75\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:34,4:0.118:38:8,1:20,2:12,22,2,2\n+K03455\t2423\t.\tA\tG\t.\t.\tAS_SB_TABLE=0,13|0,3;DP=16;ECNT=9;MBQ=34,33;MFRL=255,199;MMQ=60,60;MPOS=16;POPAF=7.30;TLOD=8.83\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:13,3:0.226:16:3,0:9,3:0,13,0,3\n+K03455\t2436\t.\tA\tG\t.\t.\tAS_SB_TABLE=0,1|0,4;DP=6;ECNT=9;MBQ=16,31;MFRL=255,240;MMQ=60,60;MPOS=4;POPAF=7.30;TLOD=16.53\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:1,4:0.725:5:0,0:0,4:0,1,0,4\n+K03455\t2438\t.\tA\tG\t.\t.\tAS_SB_TABLE=0,3|0,2;DP=6;ECNT=9;MBQ=29,33;MFRL=255,255;MMQ=60,60;MPOS=3;POPAF=7.30;TLOD=7.20\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:3,2:0.430:5:0,0:2,2:0|1:2438_A_G:2438:0,3,0,2\n+K03455\t2440\t.\tT\tC\t.\t.\tAS_SB_TABLE=0,3|0,2;DP=6;ECNT=9;MBQ=0,31;MFRL=255,255;MMQ=60,60;MPOS=1;POPAF=7.30;TLOD=7.20\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:3,2:0.430:5:0,0:0,2:0|1:2438_A_G:2438:0,3,0,2\n' |
| b |
| diff -r 3be27a9a7313 -r 287c4af133e6 test-data/Mutect2-out6.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mutect2-out6.vcf Sun May 10 17:58:00 2020 -0400 |
| b |
| b'@@ -0,0 +1,64 @@\n+##fileformat=VCFv4.2\n+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">\n+##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions of alternate alleles in the tumor">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">\n+##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele">\n+##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele">\n+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozygous and is not intended to describe called alleles">\n+##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">\n+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">\n+##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)">\n+##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher\'s Exact Test to detect strand bias.">\n+##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample NA12891 --output output.vcf --input tumor.bam --input normal.bam --reference reference.fa --QUIET true --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --min-base-quality-score 10 --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --allele-informative-reads-overlap-margin 2 --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-reads-per-alignment-start 50 --interval-set-rule UNION'..b'.\tC\tCTAT\t.\t.\tAS_SB_TABLE=19,18|4,5;DP=50;ECNT=1;MBQ=38,39;MFRL=351,362;MMQ=60,60;MPOS=34;POPAF=7.30;RPA=1,2;RU=TAT;STR;TLOD=29.75\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:11,9:0.454:20:4,4:6,4:5,6,4,5\t0/1:26,0:0.034:26:14,0:11,0:14,12,0,0\n+chr20\t863271\t.\tA\tG\t.\t.\tAS_SB_TABLE=24,10|5,4;DP=44;ECNT=1;MBQ=36,37;MFRL=347,359;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=26.85\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:8,9:0.526:17:4,5:4,4:7,1,5,4\t0/1:26,0:0.035:26:15,0:10,0:17,9,0,0\n+chr20\t863508\t.\tA\tG\t.\t.\tAS_SB_TABLE=24,20|6,6;DP=59;ECNT=1;MBQ=39,40;MFRL=343,355;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=36.80\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:11,12:0.524:23:6,6:4,6:4,7,6,6\t0/1:33,0:0.028:33:16,0:16,0:20,13,0,0\n+chr20\t863706\t.\tC\tT\t.\t.\tAS_SB_TABLE=7,25|9,11;DP=53;ECNT=2;MBQ=37,39;MFRL=341,345;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=65.75\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:0,20:0.955:20:0,12:0,7:0,0,9,11\t0/1:32,0:0.029:32:9,0:23,0:7,25,0,0\n+chr20\t863744\t.\tC\tT\t.\t.\tAS_SB_TABLE=10,24|6,6;DP=48;ECNT=2;MBQ=39,38;MFRL=341,347;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=38.56\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:8,12:0.591:20:5,7:3,5:4,4,6,6\t0/1:26,0:0.035:26:10,0:16,0:6,20,0,0\n+chr20\t863846\t.\tC\tT\t.\t.\tAS_SB_TABLE=28,10|4,3;DP=48;ECNT=2;MBQ=40,38;MFRL=348,343;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=20.26\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:17,7:0.309:24:11,5:5,2:14,3,4,3\t0/1:21,0:0.042:21:9,0:12,0:14,7,0,0\n+chr20\t863873\t.\tC\tT\t.\t.\tAS_SB_TABLE=23,11|7,3;DP=48;ECNT=2;MBQ=39,37;MFRL=353,337;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=30.15\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:21,0:0.041:21:14,0:6,0:15,6,0,0\t0/1:13,10:0.440:23:8,3:5,7:8,5,7,3\n+chr20\t864074\t.\tT\tC\t.\t.\tAS_SB_TABLE=19,20|8,3;DP=53;ECNT=1;MBQ=38,36;MFRL=344,355;MMQ=60,60;MPOS=17;POPAF=7.30;TLOD=31.98\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:13,11:0.465:24:7,9:5,2:5,8,8,3\t0/1:26,0:0.035:26:13,0:13,0:14,12,0,0\n+chr20\t864199\t.\tG\tA\t.\t.\tAS_SB_TABLE=30,18|4,9;DP=63;ECNT=1;MBQ=36,39;MFRL=343,361;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=37.97\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:15,13:0.470:28:7,7:7,6:13,2,4,9\t0/1:33,0:0.028:33:23,0:10,0:17,16,0,0\n+chr20\t864301\t.\tG\tT\t.\t.\tAS_SB_TABLE=20,17|12,6;DP=57;ECNT=1;MBQ=35,35;MFRL=344,358;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=56.37\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:12,18:0.594:30:9,12:3,6:6,6,12,6\t0/1:25,0:0.036:25:11,0:14,0:14,11,0,0\n+chr20\t864455\t.\tT\tC\t.\t.\tAS_SB_TABLE=11,17|15,17;DP=63;ECNT=2;MBQ=35,39;MFRL=343,360;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=115.14\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:0,32:0.971:32:0,16:0,16:0,0,15,17\t0/1:28,0:0.033:28:19,0:8,0:11,17,0,0\n+chr20\t864512\t.\tA\tG\t.\t.\tAS_SB_TABLE=17,22|11,15;DP=71;ECNT=2;MBQ=38,37;MFRL=344,364;MMQ=60,60;MPOS=19;POPAF=7.30;TLOD=88.07\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:14,26:0.647:40:8,12:5,14:9,5,11,15\t0/1:25,0:0.035:25:12,0:12,0:8,17,0,0\n+chr20\t864640\t.\tC\tT\t.\t.\tAS_SB_TABLE=16,18|14,14;DP=64;ECNT=2;MBQ=38,35;MFRL=339,354;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=94.78\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:0,28:0.968:28:0,11:0,17:0,0,14,14\t0/1:34,0:0.028:34:22,0:12,0:16,18,0,0\n+chr20\t864660\t.\tG\tT\t.\t.\tAS_SB_TABLE=16,15|11,11;DP=55;ECNT=2;MBQ=37,38;MFRL=340,358;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=69.72\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:0,22:0.960:22:0,8:0,12:0,0,11,11\t0/1:31,0:0.030:31:17,0:13,0:16,15,0,0\n+chr20\t865054\t.\tG\tC\t.\t.\tAS_SB_TABLE=10,8|6,4;DP=30;ECNT=1;MBQ=35,34;MFRL=347,347;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=30.15\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:9,10:0.524:19:7,6:2,4:6,3,6,4\t0/1:9,0:0.092:9:3,0:5,0:4,5,0,0\n+chr20\t865366\t.\tG\tT\t.\t.\tAS_SB_TABLE=13,13|15,11;DP=54;ECNT=1;MBQ=39,37;MFRL=343,353;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=88.44\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:0,26:0.965:26:0,14:0,10:0,0,15,11\t0/1:26,0:0.035:26:10,0:16,0:13,13,0,0\n+chr20\t865537\t.\tC\tT\t.\t.\tAS_SB_TABLE=17,29|6,3;DP=58;ECNT=1;MBQ=35,35;MFRL=350,358;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=24.37\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:19,9:0.333:28:10,4:9,5:8,11,6,3\t0/1:27,0:0.034:27:13,0:13,0:9,18,0,0\n+chr20\t865664\t.\tTC\tT\t.\t.\tAS_SB_TABLE=20,20|7,10;DP=59;ECNT=1;MBQ=35,34;MFRL=348,359;MMQ=60,60;MPOS=25;POPAF=7.30;RPA=4,3;RU=C;STR;TLOD=42.63\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:19,17:0.474:36:10,11:9,4:11,8,7,10\t0/1:21,0:0.043:21:7,0:10,0:9,12,0,0\n' |
| b |
| diff -r 3be27a9a7313 -r 287c4af133e6 test-data/chr20.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chr20.fa Sun May 10 17:58:00 2020 -0400 |
| b |
| b'@@ -0,0 +1,1050427 @@\n+>chr20\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+'..b'NNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN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| diff -r 3be27a9a7313 -r 287c4af133e6 test-data/normal.bam |
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| Binary file test-data/normal.bam has changed |
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| diff -r 3be27a9a7313 -r 287c4af133e6 test-data/tumor.bam |
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| Binary file test-data/tumor.bam has changed |