| Previous changeset 5:ed0dbb61f0e1 (2016-08-04) Next changeset 7:dc45e612bc47 (2018-06-11) |
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Commit message:
planemo upload |
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removed:
examples/assoc.hg19.vcf.gz examples/assoc.hg19.vcf.gz.tbi.gz examples/assoc.ped examples/geneset.txt examples/hg19_breast.txt examples/param.rare.disease.hg19.txt examples/rare.disease.hg19.vcf examples/rare.disease.ped.txt righe_tolte.txt |
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| diff -r ed0dbb61f0e1 -r 4e47d0245887 examples/assoc.hg19.vcf.gz |
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| Binary file examples/assoc.hg19.vcf.gz has changed |
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| diff -r ed0dbb61f0e1 -r 4e47d0245887 examples/assoc.hg19.vcf.gz.tbi.gz |
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| Binary file examples/assoc.hg19.vcf.gz.tbi.gz has changed |
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| diff -r ed0dbb61f0e1 -r 4e47d0245887 examples/assoc.ped --- a/examples/assoc.ped Thu Aug 04 05:53:40 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,984 +0,0 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| diff -r ed0dbb61f0e1 -r 4e47d0245887 examples/geneset.txt --- a/examples/geneset.txt Thu Aug 04 05:53:40 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -set1 http://set1 CICP27 HES5 AGRN VWA1 WASH7P ACAP3 UBE2J2 CDK11A RN7SL657P ATAD3B -set2 http://set2 MIR6859-1 MIR6859-2 GNB1 RER1 SKI C1orf222 ARHGEF16 SLC35E2B HES4 LINC01128 AURKAIP1 ATAD3C \ No newline at end of file |
| b |
| diff -r ed0dbb61f0e1 -r 4e47d0245887 examples/hg19_breast.txt --- a/examples/hg19_breast.txt Thu Aug 04 05:53:40 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,47796 +0,0 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|
| b |
| diff -r ed0dbb61f0e1 -r 4e47d0245887 examples/param.rare.disease.hg19.txt --- a/examples/param.rare.disease.hg19.txt Thu Aug 04 05:53:40 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,57 +0,0 @@ -#one argument per line -#I.Environmental setting ---buildver hg19 \ \ #line 1 ---nt 4 \ \ #line 2 -#--no-lib-check \ #line 3 -#--no-resource-check \ \ #line 4 - -#II. Specify the input files ---vcf-file examples/rare.disease.hg19.vcf \ #line 5 ---ped-file examples/rare.disease.ped.txt \ #line 6, or specify --indiv-pheno X:1,Y:1,Z:2 - -#III. Output setting ---out ./test1 \ #line 7 ---excel \ #line 8 ---o-vcf \ #line 10 -#--o-flanking-seq 50 \ #line 11, need large RAM memory - -#IV. QC ---gty-qual 10 \ #line 12 ---gty-dp 4 \ #line 13 ---gty-af-ref 0.05 \ #line 14 ---gty-af-het 0.25 \ #line 15 ---vcf-filter-in PASS,VQSRTrancheSNP90.00to93.00,VQSRTrancheSNP93.00to95.00,VQSRTrancheSNP95.00to97.00,VQSRTrancheSNP97.00to99.00 \ #line 16 ---seq-qual 50 \ #line 17 ---seq-mq 20 \ #line 18 ---seq-fs 60 \ #line 19 ---min-obsa 1 \ #line 20 -#V. Filtering - ---genotype-filter 1,2,6 \ #line 22 for recessive mode -#--ibs-case-filter 1000 \ #line 23, or specify 'ibdregions.txt' file ---regions-out chrX,chrY \ #line 22 ---db-filter 1kg201204,dbsnp141,ESP6500AA,ESP6500EA \ #line 26 ---rare-allele-freq 0.006 \ #line 27 ---db-filter-hard dbsnp138nf \ #line 27 ---db-gene refgene,gencode,knowngene \ #line 24 ---gene-feature-in 0,1,2,3,4,5,6 \ #line 25 ---superdup-filter \ ---gene-var-filter 4 - -#VI. Annotation ---scsnv-annot \#line 31 ---dgv-cnv-annot --candi-list ECEL1,MYBPC1,TNNI2,TNNT3,TPM2 \#line 31 ---geneset-annot cura \ #line 33 ---ppi-annot string \ #line 34 ---ppi-depth 1 \ #line 35 ---phenotype-term Arthrogryposis,Arthrogryposis+multiplex+congenita \ #line 35 ---pubmed-mining - -#VII. Prediction at variants ---db-score dbnsfp \ #line 28 ---mendel-causing-predict all ---filter-nondisease-variant \ #line 29 - -#VIII. Prediction at genes ---patho-gene-predict -#--phenolyzer-prediction \ No newline at end of file |
| b |
| diff -r ed0dbb61f0e1 -r 4e47d0245887 examples/rare.disease.hg19.vcf --- a/examples/rare.disease.hg19.vcf Thu Aug 04 05:53:40 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,530 +0,0 @@\n-##fileformat=VCFv4.0\r\n-##FILTER=<ID=LowQual,Description="Low quality">\r\n-##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">\r\n-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">\r\n-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">\r\n-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\r\n-##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">\r\n-##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">\r\n-##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">\r\n-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">\r\n-##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">\r\n-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">\r\n-##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">\r\n-##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">\r\n-##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">\r\n-##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with two (and only two) segregating haplotypes">\r\n-##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">\r\n-##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">\r\n-##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">\r\n-##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">\r\n-##SelectVariants="analysis_type=SelectVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/software/sequencing/GenomeAnalysisTK-1.0.5506/Homo_sapiens_assembly18.fasta rodBind=[/home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr1.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr2.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr3.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr4.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr5.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr6.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr7.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr8.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr9.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr10.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr11.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr12.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr13.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr14.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr15.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr16.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr17.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr18.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr19.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr20.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr21.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr22.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chrX.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chrY.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartPr'..b':99:420,0,605\t0/0:47,0:47:99:767,0,715\r\n-chr17\t9696199\trs8073531\tG\tC\t150.87\tPASS\tAC=2;AF=0.50;AN=4;DB;DP=2;Dels=0.00;HRun=2;HaplotypeScore=0.0427;MQ=118.63;MQ0=0;QD=25.14;SB=-25.88;sumGLbyD=37.63\tGT:AD:DP:GQ:PL\t0/1:18,16:31:99:420,0,606\t0/1:18,16:31:99:420,0,606\t0/0:47,0:47:99:767,0,716\r\n-chr17\t9696200\trs8074657\tC\tT\t149.89\tPASS\tAC=2;AF=0.50;AN=4;DB;DP=2;Dels=0.00;HRun=0;HaplotypeScore=0.0427;MQ=118.63;MQ0=0;QD=24.98;SB=-25.86;sumGLbyD=37.47\tGT:AD:DP:GQ:PL\t0/1:18,16:31:99:420,0,607\t0/1:18,16:31:99:420,0,607\t0/0:47,0:47:99:767,0,717\r\n-chr17\t9697803\t.\tG\tT\t225.32\tPASS\tAC=2;AF=1.00;AN=2;DP=1;Dels=0.00;HRun=1;HaplotypeScore=0.0585;MQ=80.63;MQ0=0;QD=28.17;SB=-88.69;sumGLbyD=40.55\tGT:AD:DP:GQ:PL\t0/1:18,16:31:99:420,0,608\t0/1:18,16:31:99:420,0,608\t0/0:47,0:47:99:767,0,718\r\n-chr17\t9697822\trs3915463\tA\tC\t595.48\tPASS\tAC=2;AF=1.00;AN=2;DB;DP=1;Dels=0.00;HRun=0;HaplotypeScore=0.1667;MQ=77.70;MQ0=0;QD=29.77;SB=-294.36;sumGLbyD=34.23\tGT:AD:DP:GQ:PL\t0/1:18,16:31:99:420,0,609\t0/1:18,16:31:99:420,0,609\t0/0:47,0:47:99:767,0,719\r\n-chr17\t9698307\trs4791869\tC\tT\t468.92\tPASS\tAC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;HRun=0;HaplotypeScore=0.1083;MQ=99.33;MQ0=0;QD=26.05;SB=-165.26;sumGLbyD=30.18\tGT:AD:DP:GQ:PL\t0/1:18,16:31:99:420,0,610\t0/1:18,16:31:99:420,0,610\t0/0:47,0:47:99:767,0,720\r\n-chr17\t9698396\trs4791870\tC\tT\t347.83\tPASS\tAC=2;AF=1.00;AN=2;DB;DP=3;Dels=0.00;HRun=3;HaplotypeScore=0.2494;MQ=119.94;MQ0=0;QD=26.76;SB=-181.02;sumGLbyD=32.57\tGT:AD:DP:GQ:PL\t0/1:18,16:31:99:420,0,611\t0/1:18,16:31:99:420,0,611\t0/0:47,0:47:99:767,0,721\r\n-chr17\t9698688\t.\tA\tG\t68.41\tPASS\tAC=1;AF=0.25;AN=4;DP=3;Dels=0.00;HRun=0;HaplotypeScore=0.2179;MQ=82.48;MQ0=0;QD=11.40;SB=-22.66;sumGLbyD=21.93\tGT:AD:DP:GQ:PL\t0/1:18,16:31:99:420,0,612\t0/1:18,16:31:99:420,0,612\t0/0:47,0:47:99:767,0,722\r\n-chr17\t9699974\trs9913800\tT\tC\t207.88\tPASS\tAC=2;AF=0.50;AN=4;DB;DP=2;Dels=0.00;HRun=0;HaplotypeScore=0.0000;MQ=123.42;MQ0=0;QD=23.10;SB=-94.58;sumGLbyD=29.94\tGT:AD:DP:GQ:PL\t0/1:18,16:31:99:420,0,613\t0/1:18,16:31:99:420,0,613\t0/0:47,0:47:99:767,0,723\r\n-chr17\t9700198\trs2315587\tG\tA\t414.26\tPASS\tAC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;HRun=0;HaplotypeScore=0.0000;MQ=81.74;MQ0=0;QD=31.87;SB=-164.97;sumGLbyD=35.56\tGT:AD:DP:GQ:PL\t0/1:18,16:31:99:420,0,614\t0/1:18,16:31:99:420,0,614\t0/0:47,0:47:99:767,0,724\r\n-chr17\t9701390\trs2277691\tT\tC\t442.44\tPASS\tAC=2;AF=1.00;AN=2;DB;DP=1;Dels=0.00;HRun=1;HaplotypeScore=0.0968;MQ=80.96;MQ0=0;QD=26.03;SB=-172.57;sumGLbyD=30.43\tGT:AD:DP:GQ:PL\t0/1:18,16:31:99:420,0,615\t0/1:18,16:31:99:420,0,615\t0/0:47,0:47:99:767,0,725\r\n-chr17\t9702456\trs8064616\tT\tC\t357.4\tPASS\tAC=2;AF=1.00;AN=2;DB;DP=1;Dels=0.00;HRun=2;HaplotypeScore=0.0000;MQ=83.59;MQ0=0;QD=27.49;SB=-176.79;sumGLbyD=32.09\tGT:AD:DP:GQ:PL\t0/1:18,16:31:99:420,0,616\t0/1:18,16:31:99:420,0,616\t0/0:47,0:47:99:767,0,726\r\n-chr17\t9703299\trs17207745\tG\tA\t110.55\tPASS\tAC=2;AF=1.00;AN=2;DB;DP=1;Dels=0.00;HRun=2;HaplotypeScore=0.0000;MQ=83.00;MQ0=0;QD=18.43;SB=-28.48;sumGLbyD=29.70\tGT:AD:DP:GQ:PL\t0/1:18,16:31:99:420,0,617\t0/1:18,16:31:99:420,0,617\t0/0:47,0:47:99:767,0,727\r\n-chr17\t9703383\trs2315578\tT\tC\t523.48\tPASS\tAC=4;AF=1.00;AN=4;DB;DP=3;Dels=0.00;HRun=2;HaplotypeScore=0.0000;MQ=109.12;MQ0=0;QD=30.79;SB=-262.59;sumGLbyD=35.58\tGT:AD:DP:GQ:PL\t0/1:18,16:31:99:420,0,618\t0/1:18,16:31:99:420,0,618\t0/0:47,0:47:99:767,0,728\r\n-chr17\t9707044\trs9891232\tT\tC\t401.99\tPASS\tAC=2;AF=1.00;AN=2;DB;DP=1;Dels=0.00;HRun=1;HaplotypeScore=0.0000;MQ=78.31;MQ0=0;QD=23.65;SB=-216.68;sumGLbyD=29.07\tGT:AD:DP:GQ:PL\t0/1:18,16:31:99:420,0,619\t0/1:18,16:31:99:420,0,619\t0/0:47,0:47:99:767,0,729\r\n-chr17\t9709793\trs9914056\tG\tA\t411.79\tPASS\tAC=2;AF=1.00;AN=2;DB;DP=1;Dels=0.00;HRun=0;HaplotypeScore=0.0000;MQ=86.07;MQ0=0;QD=25.74;SB=-227.09;sumGLbyD=30.16\tGT:AD:DP:GQ:PL\t0/1:18,16:31:99:420,0,620\t0/1:18,16:31:99:420,0,620\t0/0:47,0:47:99:767,0,730\r\n-chr17\t9712767\trs9912329\tA\tC\t284.87\tPASS\tAC=2;AF=0.50;AN=4;DB;DP=2;Dels=0.00;HRun=1;HaplotypeScore=0.0853;MQ=95.60;MQ0=0;QD=21.91;SB=-96.35;sumGLbyD=27.51\tGT:AD:DP:GQ:PL\t0/1:18,16:31:99:420,0,621\t0/1:18,16:31:99:420,0,621\t0/0:47,0:47:99:767,0,731\r\n' |
| b |
| diff -r ed0dbb61f0e1 -r 4e47d0245887 examples/rare.disease.ped.txt --- a/examples/rare.disease.ped.txt Thu Aug 04 05:53:40 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -1 Y 0 0 1 1 -1 Z 0 0 2 1 -1 X Y Z 1 2 \ No newline at end of file |
| b |
| diff -r ed0dbb61f0e1 -r 4e47d0245887 righe_tolte.txt --- a/righe_tolte.txt Thu Aug 04 05:53:40 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,15 +0,0 @@ -<action type="shell_command">java -jar kggseq.jar --no-lib-check --resource-update --resource resources --buildver hg19 --db-filter 1kg201305,1kg201204,1kgafr201204,1kgeur201204,1kgamr201204,1kgasn201204,dbsnp135,dbsnp137,dbsnp138,dbsnp138nf,dbsnp141,ESP6500AA,ESP6500EA,exac --genome-annot --db-gene refgene,gencode,knowngene,ensembl --db-score dbnsfp --superdup-annot --cosmic-annot --omim-annot --scsnv-annot --mouse-pheno --zebrafish-pheno --ddd-annot --mendel-causing-predict all --patho-gene-predict --dgv-cnv-annot --vcf-file examples-lite/rare.disease.hg19.vcf</action> - - -<action type="shell_command">java -Xmx4g -jar kggseq.jar --no-lib-check --no-qc --resource-update --resource resources --buildver hg19 --o-flanking-seq 10 --vcf-file examples-lite/rare.disease.hg19.vcf</action> - - - - - - - -questa riga sottostante è l'unione delle due sopra e sarà quella definitiva - - -<action type="shell_command">java -jar kggseq.jar --no-lib-check --resource resources --buildver hg19 --db-filter 1kgeur201305,1kgeas201305,1kgafr201305,1kgsas201305,1kgamr201305,1kg201305,1kg201204,1kgafr201204,1kgeur201204,1kgamr201204,1kgasn201204,dbsnp135,dbsnp137,dbsnp138,dbsnp138nf,dbsnp141,ESP6500AA,ESP6500EA,exac --genome-annot --db-gene refgene,gencode,knowngene,ensembl --db-score dbnsfp --superdup-annot --cosmic-annot --omim-annot --scsnv-annot --mouse-pheno --zebrafish-pheno --ddd-annot --mendel-causing-predict all --patho-gene-predict --dgv-cnv-annot --o-flanking-seq 10 --vcf-file examples-lite/rare.disease.hg19.vcf</action> \ No newline at end of file |