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…search Documenation update for position search
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Position Search | ||
=============== | ||
VCF Position Search is a companion tool for VCF Bulk Loader. It allows users to search variants cross all available vcf files and provides links back to Bulk Loader for variant specific filter. | ||
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.. toctree:: | ||
:maxdepth: 2 | ||
:caption: In Detail: | ||
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position_search/ps_features | ||
position_search/ps_setup | ||
position_search/ps_troubleshoot |
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Features | ||
======== | ||
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Search one variant by Variant Name or by Backbone Name and Position. | ||
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.. image:: position_search.1.search.png | ||
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Any file included in VCF Bulk Loader containing this variant will show in Search Results. Each file name can redirect to VCF Bulk Loader. | ||
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.. image:: position_search.2.results.png | ||
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The VCF Bulk Loader page will have wanted file selected and wanted variant position filled in filter criteria of Regions. | ||
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.. image:: position_search.3.link2bulkloader.png |
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How to Set Up | ||
============= | ||
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Installation of Samtools is required by VCF position search, please check `Samtools <http://www.htslib.org/>`_ for detail. | ||
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Prepare files | ||
------------- | ||
Corresponding compressed file and index file are required for each vcf file. Compressed VCF file can be generated by: | ||
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.. code:: bash | ||
bgzip -c your_vcf_file.vcf > your_vcf_file.vcf.gz | ||
Generate tbi format index: | ||
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.. code:: bash | ||
bcftools index your_vcf_file.vcf.gz | ||
Or, generate csi format index: | ||
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.. code:: bash | ||
tabix -C your_vcf_file.vcf.gz | ||
.. note:: | ||
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Please move prepared files to the directory provided in VCF Bulk Loader. | ||
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Test with test files | ||
-------------------- | ||
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Test files are included in this module and it's recommended to test before use. | ||
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.. note:: | ||
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Test files (in vcf_filter/tests/test_files/) include: test_file_1.vcf, test_file_1.vcf.gz and test_file_1.vcf.gz.csi for test1; test_short2.vcf, test_short2.vcf.gz and test_short2.vcf.gz.csi for test2. | ||
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- add both tests to VCF Bulk Loader in admin->Tripal->Extensions->VCF Filter->add as test1 and test2 | ||
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- give proper access to both tests, and check if compressed vcf file and index file are provided | ||
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- search in Position Search: search for 19p111 should give results for both test1 and test2, search for Xp9 should give result for test1 only and search for 20p120 should give result for test2 only | ||
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- delete tests in VCF Bulk Loader |
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Troubleshoot | ||
============ | ||
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If VCF Position Search is not working as expected, please check: | ||
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- if bcftools works properly | ||
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- if vcf files can be downloaded properly in VCF Bulk Loader | ||
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- if compressed vcf file (your_file.vcf.gz) and index file (your_file.vcf.gz.tbi or your_file.vcf.gz.csi) are provided in right directory | ||
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- if your compressed vcf files remain good integrity by: | ||
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.. code:: bash | ||
bcftools view your_file.vcf.gz | ||
- if one variant (e.g.: 19:111) is searchable by: | ||
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.. code:: bash | ||
cd directory_includes_vcf_fiels | ||
bcftools view --no-header -r 19:111 your_file.vcf.gz | ||
.. note:: | ||
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If you have any questions or suggestions, please contacts us at knowpulse@usask.ca. |
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##fileformat=VCFv4.0 | ||
##fileDate=20090805 | ||
##source=myImputationProgramV3.1 | ||
##reference=1000GenomesPilot-NCBI36 | ||
##phasing=partial | ||
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data"> | ||
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> | ||
##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> | ||
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> | ||
##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency"> | ||
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele"> | ||
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129"> | ||
##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership"> | ||
##FILTER=<ID=q10,Description="Quality below 10"> | ||
##FILTER=<ID=s50,Description="Less than 50% of samples have data"> | ||
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> | ||
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> | ||
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality"> | ||
##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element"> | ||
##ALT=<ID=CNV,Description="Copy number variable region"> | ||
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 | ||
19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 | ||
19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 | ||
20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. | ||
20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. | ||
20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. | ||
20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. | ||
20 1234567 microsat1 G GA,GAC 50 PASS NS=3;DP=9;AA=G;AN=6;AC=3,1 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 | ||
20 1235237 . T . . . . GT 0/0 0|0 ./. | ||
X 9 . A T 12.1 . . GT 0 0/1 1/0 | ||
X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2 | ||
X 11 rsTest2 T A,<DEL:ME:ALU> 10 q10;s50 . GT:DP:GQ .:3:10 ./.:.:. 0|2:3:. | ||
X 12 . T A 13 . . GT 0 1/0 1/1 |
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##fileformat=VCFv4.0 | ||
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> | ||
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> | ||
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> | ||
##FILTER=<ID=q10,Description="Quality below 10"> | ||
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A | ||
19 100 . GTTT G 1806 q10 DP=35 GT:GQ:DP 0/1:99:35 | ||
19 111 . C T,G 1792 PASS DP=32 GT:GQ:DP 0/1:99:32 | ||
19 111 . CAAA C 1792 PASS DP=32 GT:GQ:DP 0/1:99:32 | ||
19 120 . GA G 628 q10 DP=21 GT:GQ:DP 1/1:21:21 | ||
19 130 . G T 1016 PASS DP=22 GT:GQ:DP 0/1:99:22 | ||
19 130 . GAA GG 1016 PASS DP=22 GT:GQ:DP 0/1:99:22 | ||
19 140 . GT G 727 PASS DP=30 GT:GQ:DP 0/1:99:30 | ||
19 150 . TAAAA TA,T 246 PASS DP=10 GT:GQ:DP 1/2:12:10 | ||
19 160 . TAAAA TA,T 246 PASS DP=10 GT:GQ:DP 1/2:12:10 | ||
20 100 . GTTT G 1806 q10 DP=35 GT:GQ:DP 0/1:99:35 | ||
20 110 . CAAA C 1792 PASS DP=32 GT:GQ:DP 0/1:99:32 | ||
20 120 . GA G 628 q10 DP=21 GT:GQ:DP 1/1:21:21 | ||
20 130 . GAA G 1016 PASS DP=22 GT:GQ:DP 0/1:99:22 | ||
20 140 . GT G 727 PASS DP=30 GT:GQ:DP 0/1:99:30 | ||
20 150 . TAAAA TA,T 246 PASS DP=10 GT:GQ:DP 1/2:12:10 | ||
20 160 . TAAAA TA,TC,T 246 PASS DP=10 GT:GQ:DP 0/2:12:10 |
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