Merge pull request #55 from UofS-Pulse-Binfo/Documenation_update_pos_…

…search

Documenation update for position search

docs/configuration/optional_info.rst

@@ -22,7 +22,7 @@ Germplasm From Header
 The names of all germplasm (individuals) in this vcf file. The germplasm list must be new line separated without any header or empty lines.
 
 .. note::
-  If this textarea is not filled, the module is able to find the list from selected VCF fiels. However, waiting time of extracting germplasm list from a selected file can be sifnificant for large VCF files.
+  If this textarea is not filled, the module is able to find the list from selected VCF files. However, waiting time of extracting germplasm list from a selected file can be sifnificant for large VCF files.
   ``Loading time for a 10G VCF file will be about 3 seconds.``
 
   Since the germplasm list can be generated, it's not necessary to generate such a list for configuration otherwise. We can leave this section blank, select this file and copy generated list back to configuration.

docs/index.rst

@@ -11,3 +11,4 @@ This modules provides a form interface so users can custom filter existing VCF f
    features
    install
    configuration
+   position_search

docs/position_search.rst

@@ -0,0 +1,12 @@
+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.
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: In Detail:
+
+   position_search/ps_features
+   position_search/ps_setup
+   position_search/ps_troubleshoot

docs/position_search/ps_features.rst

@@ -0,0 +1,14 @@
+Features
+========
+
+Search one variant by Variant Name or by Backbone Name and Position.
+
+.. image:: position_search.1.search.png
+
+Any file included in VCF Bulk Loader containing this variant will show in Search Results. Each file name can redirect to VCF Bulk Loader.
+
+.. image:: position_search.2.results.png
+
+The VCF Bulk Loader page will have wanted file selected and wanted variant position filled in filter criteria of Regions.
+
+.. image:: position_search.3.link2bulkloader.png

docs/position_search/ps_setup.rst

@@ -0,0 +1,49 @@
+How to Set Up
+=============
+
+Installation of Samtools is required by VCF position search, please check `Samtools <http://www.htslib.org/>`_ for detail.
+
+Prepare files
+-------------
+Corresponding compressed file and index file are required for each vcf file. Compressed VCF file can be generated by:
+
+.. code:: bash
+
+ bgzip -c your_vcf_file.vcf > your_vcf_file.vcf.gz
+
+
+Generate tbi format index:
+
+.. code:: bash
+
+ bcftools index your_vcf_file.vcf.gz
+
+
+Or, generate csi format index:
+
+.. code:: bash
+
+ tabix -C your_vcf_file.vcf.gz
+
+
+.. note::
+
+ Please move prepared files to the directory provided in VCF Bulk Loader.
+
+Test with test files
+--------------------
+
+Test files are included in this module and it's recommended to test before use.
+
+.. note::
+
+  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.
+
+
+- add both tests to VCF Bulk Loader in admin->Tripal->Extensions->VCF Filter->add as test1 and test2
+
+- give proper access to both tests, and check if compressed vcf file and index file are provided
+
+- 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
+
+- delete tests in VCF Bulk Loader

docs/position_search/ps_troubleshoot.rst

@@ -0,0 +1,28 @@
+Troubleshoot
+============
+
+If VCF Position Search is not working as expected, please check:
+
+- if bcftools works properly
+
+- if vcf files can be downloaded properly in VCF Bulk Loader
+
+- 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
+
+- if your compressed vcf files remain good integrity by:
+
+  .. code:: bash
+
+    bcftools view your_file.vcf.gz
+
+- if one variant (e.g.: 19:111) is searchable by:
+
+  .. code:: bash
+
+    cd directory_includes_vcf_fiels
+
+    bcftools view --no-header -r 19:111 your_file.vcf.gz
+
+.. note::
+
+  If you have any questions or suggestions, please contacts us at knowpulse@usask.ca.

tests/test_files/test_short1.vcf

@@ -0,0 +1,34 @@
+##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

tests/test_files/test_short2.vcf

@@ -0,0 +1,23 @@
+##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