changes in docs format

e3ae79eb · sajvanderzeeuw · b1deafba · e3ae79eb · e3ae79eb · e3ae79eb
Commit e3ae79eb authored Dec 08, 2014 by sajvanderzeeuw
11 changed files
--- a/docs/tools/BiopetFlagstat.md
+++ b/docs/tools/BiopetFlagstat.md
+# BiopetFlagstat
+
+## Introduction
+This tool has been created to extract all the metrics from a required bam file.
+It captures for example the # of mapped reads, # of duplicates, # of mates unmapped, # of reads with a certain mapping quality etc. etc.
+
+
+## Example
+To get the help menu:
+~~~
+java -jar Biopet-0.2.0.jar tool BiopetFlagstat -h
+Usage: BiopetFlagstat [options]
+
+  -l <value> | --log_level <value>
+        Log level
+  -h | --help
+        Print usage
+  -v | --version
+        Print version
+  -I <file> | --inputFile <file>
+        out is a required file property
+  -r <chr:start-stop> | --region <chr:start-stop>
+        out is a required file property
+~~~
+
+To run the tool:
+~~~
+java -jar Biopet-0.2.0.jar tool BiopetFlagstat -I myBAM.bam
+~~~
+
+### Output
+
+|Number	|Total Flags|	Fraction|	Name|
+|------ | --------  | --------- | ------|
+|1	|862623034|	100.0000%|	All|
+|2	|861096240|	99.8230%|	Mapped|
+|3	|26506366|	3.0728%|	Duplicates|
+|4	|431233321|	49.9909%|	FirstOfPair|
+|5	|431389713|	50.0091%|	SecondOfPair|
+|6	|430909871|	49.9534%|	ReadNegativeStrand|
+|7	|0|	0.0000%|	NotPrimaryAlignment|
+|8	|862623034|	100.0000%|	ReadPaired|
+|9	|803603283|	93.1581%|	ProperPair|
+|10	|430922821|	49.9549%|	MateNegativeStrand|
+|11	|1584255|	0.1837%|	MateUnmapped|
+|12	|0|	0.0000%|	ReadFailsVendorQualityCheck|
+|13	|1380318|	0.1600%|	SupplementaryAlignment|
+|14	|1380318|	0.1600%|	SecondaryOrSupplementary|
+|15	|821996241|	95.2903%|	MAPQ>0|
+|16	|810652212|	93.9753%|	MAPQ>10|
+|17	|802852105|	93.0710%|	MAPQ>20|
+|18	|789252132|	91.4944%|	MAPQ>30|
+|19	|770426224|	89.3120%|	MAPQ>40|
+|20	|758373888|	87.9149%|	MAPQ>50|
+|21	|0|	0.0000%|	MAPQ>60|
+|22	|835092541|	96.8085%|	First normal, second read inverted (paired end orientation)|
+|23	|765156|	0.0887%|	First normal, second read normal|
+|24	|624090|	0.0723%|	First inverted, second read inverted|
+|25	|11537740|	1.3375%|	First inverted, second read normal|
+|26	|1462857|	0.1696%|	Mate in same strand|
+|27	|11751691|	1.3623%|	Mate on other chr|
\ No newline at end of file
--- a/docs/tools/CheckAllelesVcfInBam.md
+++ b/docs/tools/CheckAllelesVcfInBam.md
+# CheckAllelesVcfInBam
+
+## Introduction
+This tool has been written to check the allele frequency in BAM files.
+
+## Example
+To get the help menu:
+~~~
+java -jar Biopet-0.2.0.jar tool CheckAllelesVcfInBam -h
+Usage: CheckAllelesVcfInBam [options]
+
+  -l <value> | --log_level <value>
+        Log level
+  -h | --help
+        Print usage
+  -v | --version
+        Print version
+  -I <file> | --inputFile <file>
+        
+  -o <file> | --outputFile <file>
+        
+  -s <value> | --sample <value>
+        
+  -b <value> | --bam <value>
+        
+  -m <value> | --min_mapping_quality <value>
+~~~
+
+To run the tool:
+~~~
+java -jar Biopet-0.2.0.jar tool CheckAllelesVcfInBam --inputFile myVCF.vcf \
+--bam myBam1.bam --sample bam_sample1 --outputFile myAlleles.vcf
+
+~~~
+Note that the tool can run multiple BAM files at once.
+The only thing one needs to make sure off is matching the `--bam` and `--sample` in that same order.
+
+For multiple bam files:
+~~~
+java -jar Biopet-0.2.0.jar tool CheckAllelesVcfInBam --inputFile myVCF.vcf \
+--bam myBam1.bam --sample bam_sample1 --bam myBam2.bam --sample bam_sample2 \
+--bam myBam3.bam --sample bam_sample3 --outputFile myAlleles.vcf
+~~~
+
+## Output
+outputFile = VCF file which contains an extra field with the allele frequencies per sample given to the tool.
--- a/docs/tools/ExtractAlignedFastq.md
+++ b/docs/tools/ExtractAlignedFastq.md
+# ExtractAlignedFastq
+
+## Introduction
+This tool extracts reads from a BAM file based on alignment intervals.
+E.g if one is interested in a specific location this tool extracts the full reads from the location.
+The tool is also very usefull to create test data sets.
+
+
+## Example
+To get the help menu:
+~~~
+java -jar Biopet-0.2.0.jar tool ExtractAlignedFastq -h
+ExtractAlignedFastq - Select aligned FASTQ records
+      
+Usage: ExtractAlignedFastq [options]
+
+  -l <value> | --log_level <value>
+        Log level
+  -h | --help
+        Print usage
+  -v | --version
+        Print version
+  -I <bam> | --input_file <bam>
+        Input BAM file
+  -r <interval> | --interval <interval>
+        Interval strings
+  -i <fastq> | --in1 <fastq>
+        Input FASTQ file 1
+  -j <fastq> | --in2 <fastq>
+        Input FASTQ file 2 (default: none)
+  -o <fastq> | --out1 <fastq>
+        Output FASTQ file 1
+  -p <fastq> | --out2 <fastq>
+        Output FASTQ file 2 (default: none)
+  -Q <value> | --min_mapq <value>
+        Minimum MAPQ of reads in target region to remove (default: 0)
+  -s <value> | --read_suffix_length <value>
+        Length of common suffix from each read pair (default: 0)
+
+This tool creates FASTQ file(s) containing reads mapped to the given alignment intervals.
+~~~
+
+To run the tool:
+~~~
+java -jar Biopet-0.2.0.jar tool ExtractAlignedFastq \
+--input_file myBam.bam --in1 myFastq_R1.fastq --out1 myOutFastq_R1.fastq --interval myTarget.bed
+~~~
+* Note that this tool works for single end and paired end data. The above example can be easily extended for paired end data.
+The only thing one should add is: `--in2 myFastq_R2.fastq --out2 myOutFastq_R2.fastq`
+* The interval is just a genomic position or multiple genomic positions wherefrom one wants to extract the reads.
+
+
+## Output
+The output of this tool will be fastq files containing only mapped reads with the given alignment intervals extracted from the bam file.
\ No newline at end of file
--- a/docs/tools/FastqSplitter.md
+++ b/docs/tools/FastqSplitter.md
+# FastqSplitter
+
+## Introduction
+This tool splits a fastq files based on the number of output files specified. So if one specifies 5 output files it will split the fastq
+into 5 files. This can be very usefull if one wants to use chunking option in one of our pipelines, we can generate the exact amount of fastqs
+needed for the number of chunks specified. Note that this will be automatically done inside the pipelines.  
+
+
+## Example
+To get the help menu:
+~~~
+java -jar Biopet-0.2.0.jar tool FastqSplitter -h
+Usage: FastqSplitter [options]
+
+  -l <value> | --log_level <value>
+        Log level
+  -h | --help
+        Print usage
+  -v | --version
+        Print version
+  -I <file> | --inputFile <file>
+        out is a required file property
+  -o <file> | --output <file>
+        out is a required file property
+~~~
+To run the tool:
+~~~
+java -jar Biopet-0.2.0.jar tool FastqSplitter --inputFile myFastq.fastq \
+--output mySplittedFastq_1.fastq --output mySplittedFastq_2.fastq \
+--output mySplittedFastq_3.fastq
+~~~
+The above invocation will split the input in 3 equally divided fastq files.
+
+## Output
+Multiple fastq files based on the number of outputFiles specified.
\ No newline at end of file
--- a/docs/tools/FindRepeatsPacBio.md
+++ b/docs/tools/FindRepeatsPacBio.md
+# FindRepeatsPacBio
+
+## Introduction
+This tool looks and annotates repeat regions inside a BAM file. It extracts the regions of interest from a bed file and then intersects
+those regions with the BAM file. On those extracted regions the tool will perform a
+ Mpileup and counts all insertions/deletions etc. etc. for that specific location on a per read basis.
+
+
+## Example
+To get the help menu:
+~~~
+ java -jar Biopet-0.2.0-DEV-801b72ed.jar tool FindRepeatsPacBio -h
+Usage: FindRepeatsPacBio [options]
+
+  -l <value> | --log_level <value>
+        Log level
+  -h | --help
+        Print usage
+  -v | --version
+        Print version
+  -I <file> | --inputBam <file>
+        
+  -b <file> | --inputBed <file>
+        output file, default to stdout
+~~~
+
+To run the tool:
+~~~
+ java -jar Biopet-0.2.0.jar tool FindRepeatsPacBio --inputBam myInputbam.bam \
+--inputBed myRepeatRegions.bed > mySummary.txt
+~~~
+Since the default output of the program is printed in stdout we can use > to write the output to a text file.
+
+
+## Output
+The Output is a tab delimited text file which looks like this:
+
+|chr  |startPos|stopPos |Repeat_seq|repeatLength|original_Repeat_readLength|
+|-----|--------|--------|----------|------------|--------------------------|
+|chr4 |3076603 |3076667 |CAG       |3     	|65                        |
+|chr4 |3076665 |3076667 |GCC       |3           |3                         |
+|chrX |66765158|66765261|GCA       |3           |104                       |
+
+table continues below:
+
+|Calculated_repeat_readLength|minLength|maxLength|inserts                              |
+|----------------------------|---------|---------|-------------------------------------|
+|61,73,68                    |61       |73       |GAC,G,T/A,C,G,G,A,G,A,G/C,C,C,A,C,A,G|
+|3,3,3                       |3        |3        |//                                   |
+|98                          |98       |98       |A,G,G                                |
+
+table continues below:
+
+|deletions           |notSpan|
+|--------------------|-------|
+|1,1,2,1,1,1,2//2,1,1|0      |
+|//                  |0      |
+|1,1,1,1,1,1,2,1     |0      |
\ No newline at end of file
--- a/docs/tools/MergeAlleles.md
+++ b/docs/tools/MergeAlleles.md
+# MergeAlleles
+
+## Introduction
+This tool is used to merge overlapping alleles. 
+
+
+## Example
+To get the help menu:
+~~~
+java -jar Biopet-0.2.0.jar tool MergeAlleles -h
+Usage: MergeAlleles [options]
+
+  -l <value> | --log_level <value>
+        Log level
+  -h | --help
+        Print usage
+  -v | --version
+        Print version
+  -I <file> | --inputVcf <file>
+        
+  -o <file> | --outputVcf <file>
+        
+  -R <file> | --reference <file>
+~~~
+
+To run the tool:
+~~~
+java -jar Biopet-0.2.0-DEV-801b72ed.jar tool MergeAlleles \
+--inputVcf myInput.vcf --outputVcf myOutput.vcf \
+--reference /H.Sapiens/hg19/reference.fa
+~~~
+
+## Output
+The output of this tool is a VCF file like format containing the merged Alleles only.
\ No newline at end of file
--- a/docs/tools/VcfFilter.md
+++ b/docs/tools/VcfFilter.md
+# VcfFilter
+
+## Introduction
+This tool enables a user to filter VCF files. For example on sample depth and/or total depth.
+It can also be used to filter out the reference calls and/or minimum number of sample passes.
+There is a wide set of options which one can use to change the filter settings.
+
+## Example
+To open the help menu:
+~~~
+java -jar Biopet-0.2.0.jar tool VcfFilter -h
+Usage: VcfFilter [options]
+
+  -l <value> | --log_level <value>
+        Log level
+  -h | --help
+        Print usage
+  -v | --version
+        Print version
+  -I <file> | --inputVcf <file>
+        Input vcf file
+  -o <file> | --outputVcf <file>
+        Output vcf file
+  --minSampleDepth <int>
+        Min value for DP in genotype fields
+  --minTotalDepth <int>
+        Min value of DP field in INFO fields
+  --minAlternateDepth <int>
+        Min value of AD field in genotype fields
+  --minSamplesPass <int>
+        Min number of samples to pass --minAlternateDepth, --minBamAlternateDepth and --minSampleDepth
+  --minBamAlternateDepth <int>
+  --denovoInSample <sample>
+        Only show variants that contain unique alleles in compete set for given sample
+  --mustHaveVariant <sample>
+        Given sample must have 1 alternative allele
+  --diffGenotype <sample:sample>
+        Given samples must have a different genotype
+  --filterHetVarToHomVar <sample:sample>
+        If variants in sample 1 are heterogeneous and alternative alleles are homogeneous in sample 2 variants are filtered
+  --filterRefCalls
+        Filter when there are only ref calls
+  --filterNoCalls
+        Filter when there are only no calls
+  --minQualscore <value>
+        Min qual score
+~~~
+
+To run the tool:
+~~~
+java -jar Biopet-0.2.0.jar tool VcfFilter --inputVcf myInput.vcf \
+--outputVcf myOutput.vcf --filterRefCalls --minSampleDepth 
+~~~
+
+## Output
+The output is a vcf file containing the filters specified values.
\ No newline at end of file
--- a/docs/tools/VcfToTsv.md
+++ b/docs/tools/VcfToTsv.md
+# VcfToTsv
+
+## Introduction
+This tool enables a user to convert a vcf file to a tab delimited file (TSV). 
+This can be very usefull since some programs only accept a TSV for downstream analysis.
+It gets rid of the vcf header and parses all data columns in a nice TSV file.
+There is also a possibility to only select some specific fields from you vcf and only parse those fields to a TSV.
+
+## Example
+To open the help menu:
+~~~
+java -jar Biopet-0.2.0.jar tool VcfToTsv -h
+Usage: VcfToTsv [options]
+
+  -l <value> | --log_level <value>
+        Log level
+  -h | --help
+        Print usage
+  -v | --version
+        Print version
+  -I <file> | --inputFile <file>
+        
+  -o <file> | --outputFile <file>
+        output file, default to stdout
+  -f <value> | --field <value>
+        
+  -i <value> | --info_field <value>
+        
+  --all_info
+        
+  --all_format
+        
+  -s <value> | --sample_field <value>
+        
+  -d | --disable_defaults
+~~~
+
+To run the tool:
+~~~
+java -jar Biopet-0.2.0.jar tool VcfToTsv --inputFile myVCF.vcf \
+--outputFile my_tabDelimited_VCF.tsv --all_info
+~~~
+
+## Output
+The output of this tool is a TSV file produced from the input vcf file. 
+Depending on which options are enabled their could be some fields discarded.
\ No newline at end of file
--- a/docs/tools/WipeReads.md
+++ b/docs/tools/WipeReads.md
+# WipeReads
+
+## Introduction
+WipeReads is a tool for removing reads from indexed BAM files.
+It respects pairing information and can be set to remove reads whose duplicate
+maps outside of the target region. The main use case is to remove reads mapping
+to known ribosomal RNA regions (using a supplied BED file containing intervals for these regions).
+
+## Example
+To open the help menu:
+~~~
+java -jar Biopet-0.2.0.jar tool WipeReads -h
+
+WipeReads - Region-based reads removal from an indexed BAM file
+      
+Usage: WipeReads [options]
+
+  -l <value> | --log_level <value>
+        Log level
+  -h | --help
+        Print usage
+  -v | --version
+        Print version
+  -I <bam> | --input_file <bam>
+        Input BAM file
+  -r <bed/gtf/refflat> | --interval_file <bed/gtf/refflat>
+        Interval BED file
+  -o <bam> | --output_file <bam>
+        Output BAM file
+  -f <bam> | --discarded_file <bam>
+        Discarded reads BAM file (default: none)
+  -Q <value> | --min_mapq <value>
+        Minimum MAPQ of reads in target region to remove (default: 0)
+  -G <rgid> | --read_group <rgid>
+        Read group IDs to be removed (default: remove reads from all read groups)
+  --limit_removal
+        Whether to remove multiple-mapped reads outside the target regions (default: yes)
+  --no_make_index
+        Whether to index output BAM file or not (default: yes)
+
+GTF-only options:
+  -t <gtf_feature_type> | --feature_type <gtf_feature_type>
+        GTF feature containing intervals (default: exon)
+
+Advanced options:
+  --bloom_size <value>
+        Expected maximum number of reads in target regions (default: 7e7)
+  --false_positive <value>
+        False positive rate (default: 4e-7)
+
+This tool will remove BAM records that overlaps a set of given regions.
+By default, if the removed reads are also mapped to other regions outside
+the given ones, they will also be removed.
+~~~
+
+To run the tool:
+~~~
+java -jar Biopet-0.2.0.jar tool WipeReads --input_file myBam.bam \
+--interval_file myRibosomal_regions.bed --output_file myFilteredBam.bam
+~~~
+
+## Output
+This tool outputs a bam file containing all the reads not inside a ribosomal region.
+And optionally a bam file with only the ribosomal reads
--- a/docs/tools/sagetools.md
+++ b/docs/tools/sagetools.md
@@ -3,6 +3,7 @@ These tools are written to create the appropriate files for the SAGE pipeline.
 Note that these tools are already implemented in the pipeline.

 ## SageCountFastq
+To open the help menu:
 ~~~
 java -jar Biopet-0.2.0.jar tool SageCreateLibrary -h
 Usage: SageCountFastq [options]
@@ -19,6 +20,7 @@ Usage: SageCountFastq [options]
 ~~~

 ## SageCreateLibrary
+To open the help menu:
 ~~~
 java -jar Biopet-0.2.0.jar tool SageCreateLibrary -h
 Usage: SageCreateLibrary [options]
@@ -42,10 +44,10 @@ Usage: SageCreateLibrary [options]
  --noAntiTagsOutput <file>
        
  --allGenesOutput <file>
-
 ~~~

 ## SageCreateTagCounts
+To open the help menu:
 ~~~
 java -jar Biopet-0.2.0.jar tool SageCreateTagCounts -h
 Usage: SageCreateTagCounts [options]

--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -11,10 +11,17 @@ pages:
 - ['tools/BastyGenerateFasta.md','tools','BastyGenerateFasta']
 - ['tools/bedtointerval.md','tools','BedToInterval']
 - ['tools/bedtoolscoveragetocounts.md','tools','BedtoolsCoverageToCounts']
+- ['tools/BiopetFlagstat.md','tools','BiopetFlagstat']
+- ['tools/CheckAllelesVcfInBam.md','tools','CheckAllelesVcfInBam']
+- ['tools/ExtractAlignedFastq.md','tools','ExtractAlignedFastq']
+- ['tools/FastqSplitter.md', 'tools','FastqSplitter']
+- ['tools/FindRepeatsPacBio.md','tools','FindRepeatsPacBio']
+- ['tools/VcfFilter.md','tools','VcfFilter']
 - ['tools/MpileupToVcf.md', 'tools', 'MpileupToVcf']
 - ['tools/sagetools.md', 'tools', 'Sagetools']
+- ['tools/WipeReads.md', 'tools', 'WipeReads']
 - ['cluster/oge.md', 'OpenGridEngine']
 - ['about.md', 'About']
 - ['license.md', 'License']
 theme: readthedocs
-repo_url: https://git.lumc.nl/biopet/biopet
+repo_url: https://git.lumc.nl/biopet/biopet
\ No newline at end of file