Mercurial > repos > iuc > rna_starsolo
changeset 20:45795f582ae9 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
author | iuc |
---|---|
date | Tue, 27 Aug 2024 14:11:53 +0000 |
parents | 42ce70172b72 |
children | |
files | macros.xml rg_rnaStarSolo.xml test-data/filtered3.vcf test-data/filtered4.bam test-data/rnastar_test.log test-data/rnastar_test_splicejunctions_wasp.bed |
diffstat | 6 files changed, 497 insertions(+), 105 deletions(-) [+] |
line wrap: on
line diff
--- a/macros.xml Wed Feb 14 09:04:09 2024 +0000 +++ b/macros.xml Tue Aug 27 14:11:53 2024 +0000 @@ -5,7 +5,7 @@ the index versions in sync, but you should manually update @IDX_VERSION_SUFFIX@ --> <!-- STAR version to be used --> <token name="@TOOL_VERSION@">2.7.11a</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">21.01</token> <!-- STAR index version compatible with this version of STAR This is the STAR version that introduced the index structure expected @@ -17,16 +17,14 @@ <token name="@IDX_VERSION@">2.7.4a</token> <token name="@IDX_VERSION_SUFFIX@">2</token> <token name="@IDX_DATA_TABLE@">rnastar_index2x_versioned</token> - <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">star</requirement> <requirement type="package" version="1.18">samtools</requirement> <requirement type="package" version="1.13">gzip</requirement> - <yield /> + <yield/> </requirements> </xml> - <xml name="edam"> <edam_topics> <edam_topic>topic_3170</edam_topic> @@ -36,20 +34,16 @@ <edam_operation>operation_0292</edam_operation> </edam_operations> </xml> - <xml name="index_selection" token_with_gene_model="0"> - <param argument="--genomeDir" type="select" - label="Select reference genome" - help="If your genome of interest is not listed, contact the Galaxy team"> + <param argument="--genomeDir" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> <options from_data_table="@IDX_DATA_TABLE@"> - <filter type="static_value" column="4" value="@WITH_GENE_MODEL@" /> - <filter type="static_value" column="5" value="@IDX_VERSION@" /> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No indexes are available for the selected input dataset" /> + <filter type="static_value" column="4" value="@WITH_GENE_MODEL@"/> + <filter type="static_value" column="5" value="@IDX_VERSION@"/> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No indexes are available for the selected input dataset"/> </options> </param> </xml> - <token name="@FASTQ_GZ_OPTION@"> --readFilesCommand zcat </token> @@ -59,9 +53,9 @@ </citations> </xml> <xml name="SJDBOPTIONS"> - <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="false" help="Exon junction information for mapping splices"/> - <param argument="--sjdbGTFfeatureExon" type="text" value="exon" label="Elements to use from the gene model to use for splice junctions" help="By default and for almost all cases: 'exon', referring to finding junctions at the RNA splice sites. This can optionally be changed to allow splicing at other levels, such as 'gene', 'transcript', 'CDS'."/> - <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/> + <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="false" help="Exon junction information for mapping splices"/> + <param argument="--sjdbGTFfeatureExon" type="text" value="exon" label="Elements to use from the gene model to use for splice junctions" help="By default and for almost all cases: 'exon', referring to finding junctions at the RNA splice sites. This can optionally be changed to allow splicing at other levels, such as 'gene', 'transcript', 'CDS'."/> + <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/> </xml> <xml name="dbKeyActions"> <actions> @@ -80,7 +74,7 @@ </when> <when value="history"> <action type="metadata" name="dbkey"> - <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" /> + <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey"/> </action> </when> </conditional> @@ -135,7 +129,7 @@ && #end if ]]></token> - <token name="@REFGENOMEHANDLING@" ><![CDATA[ + <token name="@REFGENOMEHANDLING@"><![CDATA[ --runThreadN \${GALAXY_SLOTS:-4} --genomeLoad NoSharedMemory --genomeDir @@ -154,7 +148,7 @@ #end if #end if ]]></token> - <token name="@READSHANDLING@" ><![CDATA[ + <token name="@READSHANDLING@"><![CDATA[ ## Check that the input pairs are of the same type ## otherwise STARsolo will run for a long time and then error out. ## We consume either repeats of two inputs R1 + R2 @@ -183,59 +177,57 @@ @FASTQ_GZ_OPTION@ #end if ]]></token> - <token name="@LIMITS@" ><![CDATA[ + <token name="@LIMITS@"><![CDATA[ --limitOutSJoneRead $getVar('algo.params.junction_limits.limitOutSJoneRead', $getVar('solo.junction_limits.limitOutSJoneRead', 1000)) --limitOutSJcollapsed $getVar('algo.params.junction_limits.limitOutSJcollapsed', $getVar('solo.junction_limits.limitOutSJcollapsed', 1000000)) --limitSjdbInsertNsj $getVar('algo.params.junction_limits.limitSjdbInsertNsj', $getVar('solo.junction_limits.limitSjdbInsertNsj', 1000000)) ]]></token> <xml name="ref_selection"> - <param argument="--genomeFastaFiles" type="data" format="fasta,fasta.gz" label="Select a reference genome" /> - <param argument="--genomeSAindexNbases" type="integer" min="2" max="16" value="14" label="Length of the SA pre-indexing string" help="Typically between 10 and 15. Longer strings will use much more memory, but allow faster searches. For small genomes, the parameter --genomeSAindexNbases must be scaled down to min(14, log2(GenomeLength)/2 - 1)"/> + <param argument="--genomeFastaFiles" type="data" format="fasta,fasta.gz" label="Select a reference genome"/> + <param argument="--genomeSAindexNbases" type="integer" min="2" max="16" value="14" label="Length of the SA pre-indexing string" help="Typically between 10 and 15. Longer strings will use much more memory, but allow faster searches. For small genomes, the parameter --genomeSAindexNbases must be scaled down to min(14, log2(GenomeLength)/2 - 1)"/> </xml> - <xml name="stdio" > + <xml name="stdio"> <stdio> <regex match="FATAL error" source="both" level="fatal"/> <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/> <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/> <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/> - <yield /> + <yield/> </stdio> </xml> <xml name="input_selection"> - <conditional name="input_types" > - <param name="use" type="select" label="Input Type" > - <option value="repeat" >Separate barcode and cDNA reads</option> - <option value="list_paired" >Paired collection of barcode and cDNA reads</option> + <conditional name="input_types"> + <param name="use" type="select" label="Input Type"> + <option value="repeat">Separate barcode and cDNA reads</option> + <option value="list_paired">Paired collection of barcode and cDNA reads</option> </param> <when value="repeat"> - <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" multiple="true" - label="RNA-Seq FASTQ/FASTA file, Barcode reads" /> - <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input2" type="data" multiple="true" - label="RNA-Seq FASTQ/FASTA file, cDNA reads"/> + <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" multiple="true" label="RNA-Seq FASTQ/FASTA file, Barcode reads"/> + <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input2" type="data" multiple="true" label="RNA-Seq FASTQ/FASTA file, cDNA reads"/> </when> <when value="list_paired"> - <param name="input_collection" collection_type="paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="Collection of Pairs" /> + <param name="input_collection" collection_type="paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="Collection of Pairs"/> </when> </conditional> </xml> <xml name="input_selection_smart_seq"> - <conditional name="input_types_smart_seq" > - <param name="use" type="select" label="Input Type" > - <option value="list_single_end" >Single-end FASTQ collection</option> - <option value="list_paired_end" >Paired FASTQ collection</option> + <conditional name="input_types_smart_seq"> + <param name="use" type="select" label="Input Type"> + <option value="list_single_end">Single-end FASTQ collection</option> + <option value="list_paired_end">Paired FASTQ collection</option> </param> <when value="list_single_end"> - <param name="single_end_collection" collection_type="list" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="List of single-end FASTQ files" /> + <param name="single_end_collection" collection_type="list" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="List of single-end FASTQ files"/> </when> <when value="list_paired_end"> - <param name="paired_end_collection" collection_type="list:paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="List of paired-end FASTQ files" /> + <param name="paired_end_collection" collection_type="list:paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="List of paired-end FASTQ files"/> </when> </conditional> </xml> <xml name="umidedup_options"> <option value="1MM_All" selected="true">Collapse all UMIs with 1 mismatch distance to each other (1MM_All)</option> - <option value="1MM_Directional_UMItools" >Directional method from the UMI-tool</option> - <option value="1MM_Directional" >Directional with stringent UMI deduplication</option> + <option value="1MM_Directional_UMItools">Directional method from the UMI-tool</option> + <option value="1MM_Directional">Directional with stringent UMI deduplication</option> </xml> <xml name="anchor_types"> <option value="0">Read start</option> @@ -244,16 +236,16 @@ <option value="3">Adapter end</option> </xml> <xml name="cb_match_wl_common"> - <option value="Exact" >Exact</option> - <option value="1MM" >Single match (1MM)</option> + <option value="Exact">Exact</option> + <option value="1MM">Single match (1MM)</option> </xml> <xml name="cb_match_wl_cellranger"> - <option value="1MM_multi" selected="true" >Multiple matches (CellRanger 2, 1MM_multi)</option> - <option value="1MM_multi_pseudocounts" >Multiple matches (CellRanger 3, 1MM_multi_pseudocounts)</option> - <option value="1MM_multi_Nbase_pseudocounts" >Multimatching to WL is allowed for CBs with N-bases (CellRanger 3, 1MM_multi_Nbase_pseudocounts)</option> + <option value="1MM_multi" selected="true">Multiple matches (CellRanger 2, 1MM_multi)</option> + <option value="1MM_multi_pseudocounts">Multiple matches (CellRanger 3, 1MM_multi_pseudocounts)</option> + <option value="1MM_multi_Nbase_pseudocounts">Multimatching to WL is allowed for CBs with N-bases (CellRanger 3, 1MM_multi_Nbase_pseudocounts)</option> </xml> <xml name="solo_adapter_params"> - <param argument="--soloAdapterSequence" type="text" value="-" label="Adapter sequence to anchor barcodes." > + <param argument="--soloAdapterSequence" type="text" value="-" label="Adapter sequence to anchor barcodes."> <sanitizer> <valid initial="string.digits"> <add value="-"/> @@ -265,11 +257,11 @@ </valid> </sanitizer> </param> - <param argument="--soloAdapterMismatchesNmax" type="integer" min="1" value="1" label="Maximum number of mismatches allowed in adapter sequence" /> - <param argument="--clipAdapterType" type="select" > - <option value="Hamming" selected="true" >Adapter clipping based on Hamming distance</option> - <option value="CellRanger4" >5p and 3p adapter clipping similar to CellRanger4</option> - <option value="None" >No adapter clipping</option> + <param argument="--soloAdapterMismatchesNmax" type="integer" min="1" value="1" label="Maximum number of mismatches allowed in adapter sequence"/> + <param argument="--clipAdapterType" type="select"> + <option value="Hamming" selected="true">Adapter clipping based on Hamming distance</option> + <option value="CellRanger4">5p and 3p adapter clipping similar to CellRanger4</option> + <option value="None">No adapter clipping</option> </param> </xml> <xml name="common_SAM_attributes"> @@ -284,14 +276,14 @@ </xml> <xml name="limits"> <section name="junction_limits" title="Junction Limits" expanded="false"> - <param argument="--limitOutSJoneRead" type="integer" min="1" value="1000" label="Maximum number of junctions for one read (including all multimappers)" /> - <param argument="--limitOutSJcollapsed" type="integer" min="1" value="1000000" label="Maximum number of collapsed junctions" /> - <param argument="--limitSjdbInsertNsj" type="integer" min="0" value="1000000" label="Maximum number of inserts to be inserted into the genome on the fly." /> + <param argument="--limitOutSJoneRead" type="integer" min="1" value="1000" label="Maximum number of junctions for one read (including all multimappers)"/> + <param argument="--limitOutSJcollapsed" type="integer" min="1" value="1000000" label="Maximum number of collapsed junctions"/> + <param argument="--limitSjdbInsertNsj" type="integer" min="0" value="1000000" label="Maximum number of inserts to be inserted into the genome on the fly."/> </section> </xml> <xml name="outCountActions"> <actions> - <action name="column_names" type="metadata" default="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" /> + <action name="column_names" type="metadata" default="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand"/> <expand macro="dbKeyAction"/> </actions> </xml> @@ -304,7 +296,7 @@ </param> <when value="None"> <!-- This is necessary for the filtering of output --> - <param name="outWigStrand" type="hidden" value="false" /> + <param name="outWigStrand" type="hidden" value="false"/> </when> <when value="bedGraph"> <expand macro="outWigParams"/> @@ -352,73 +344,92 @@ <xml name="outWigOutputs"> <data format="bedgraph" name="signal_unique_str1" label="${tool.name} on ${on_string}: Coverage Uniquely mapped strand 1" from_work_dir="Signal.Unique.str1.out"> <filter>outWig['outWigType'] != "None"</filter> - <expand macro="dbKeyActions" /> + <expand macro="dbKeyActions"/> <change_format> - <when input="outWig.outWigType" value="wiggle" format="wig" /> + <when input="outWig.outWigType" value="wiggle" format="wig"/> </change_format> </data> <data format="bedgraph" name="signal_uniquemultiple_str1" label="${tool.name} on ${on_string}: Coverage Uniquely + Multiple mapped strand 1" from_work_dir="Signal.UniqueMultiple.str1.out"> <filter>outWig['outWigType'] != "None"</filter> - <expand macro="dbKeyActions" /> + <expand macro="dbKeyActions"/> <change_format> - <when input="outWig.outWigType" value="wiggle" format="wig" /> + <when input="outWig.outWigType" value="wiggle" format="wig"/> </change_format> </data> <data format="bedgraph" name="signal_unique_str2" label="${tool.name} on ${on_string}: Coverage Uniquely mapped strand 2" from_work_dir="Signal.Unique.str2.out"> <filter>outWig['outWigType'] != "None" and outWig['outWigStrand']</filter> - <expand macro="dbKeyActions" /> + <expand macro="dbKeyActions"/> <change_format> - <when input="outWig.outWigType" value="wiggle" format="wig" /> + <when input="outWig.outWigType" value="wiggle" format="wig"/> </change_format> </data> <data format="bedgraph" name="signal_uniquemultiple_str2" label="${tool.name} on ${on_string}: Coverage Uniquely + Multiple mapped strand 2" from_work_dir="Signal.UniqueMultiple.str2.out"> <filter>outWig['outWigType'] != "None" and outWig['outWigStrand']</filter> - <expand macro="dbKeyActions" /> + <expand macro="dbKeyActions"/> <change_format> - <when input="outWig.outWigType" value="wiggle" format="wig" /> + <when input="outWig.outWigType" value="wiggle" format="wig"/> </change_format> </data> </xml> <xml name="quantMode"> <conditional name="quantmode_output"> - <param argument="--quantMode" type="select" - label="Per gene/transcript output" - help="STAR can provide analysis results not only with respect to the reference genome, but also with respect to genes and transcripts described by a gene model. Note: This functionality requires either the selection above of a cached index with a gene model, or a gene model provided alongside the index/reference genome in GTF or GFF3 format!"> + <param argument="--quantMode" type="select" label="Per gene/transcript output" help="STAR can provide analysis results not only with respect to the reference genome, but also with respect to genes and transcripts described by a gene model. Note: This functionality requires either the selection above of a cached index with a gene model, or a gene model provided alongside the index/reference genome in GTF or GFF3 format!"> <option value="-">No per gene or transcript output</option> <option value="GeneCounts">Per gene read counts (GeneCounts)</option> <option value="TranscriptomeSAM">Transcript-based BAM output (TranscriptomeSAM)</option> <option value="TranscriptomeSAM GeneCounts">Both per gene read counts and transcript-based BAM output (TranscriptomeSAM GeneCounts)</option> </param> - <when value="-" /> - <when value="GeneCounts" /> + <when value="-"/> + <when value="GeneCounts"/> <when value="TranscriptomeSAM"> - <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend" - label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?" - help="You will need to exclude alignments with indels and soft-clipped bases from the transcriptome BAM output for compatibility with certain transcript quantification tools, most notably RSEM. If you are using a tool, like eXpress, that can deal with indels and soft-clipped bases, you can achieve better results by leaving this option disabled." /> + <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend" label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?" help="You will need to exclude alignments with indels and soft-clipped bases from the transcriptome BAM output for compatibility with certain transcript quantification tools, most notably RSEM. If you are using a tool, like eXpress, that can deal with indels and soft-clipped bases, you can achieve better results by leaving this option disabled."/> </when> <when value="TranscriptomeSAM GeneCounts"> - <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend" - label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?" - help="You will need to exclude alignments with indels and soft-clipped bases from the transcriptome BAM output for compatibility with certain transcript quantification tools, most notably RSEM. If you are using a tool, like eXpress, that can deal with indels and soft-clipped bases, you can achieve better results by leaving this option disabled." /> + <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend" label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?" help="You will need to exclude alignments with indels and soft-clipped bases from the transcriptome BAM output for compatibility with certain transcript quantification tools, most notably RSEM. If you are using a tool, like eXpress, that can deal with indels and soft-clipped bases, you can achieve better results by leaving this option disabled."/> </when> </conditional> </xml> <xml name="quantModeNoGTF"> <conditional name="quantmode_output"> - <param argument="--quantMode" type="select" - label="Per gene/transcript output"> + <param argument="--quantMode" type="select" label="Per gene/transcript output"> <option value="-">No per gene or transcript output as no GTF was provided</option> </param> - <when value="-" /> + <when value="-"/> </conditional> </xml> <xml name="outSAMmapqUnique"> <!-- MAPQ 255 is the default in STAR (coming from tophat behaviour and compatibility for Cufflinks) but it is a problematic value - according to SAM/BAM specs it means "undefined". - Using 255 as the max mapq causes problem with modern downstream tools like mutect2: https://sites.duke.edu/workblog/2021/08/18/star-rnaseq-gatk-mutect2/ and 60 has become an inofficial replacement for 255. --> - <param argument="--outSAMmapqUnique" type="integer" value="60" min="0" max="255" - label="MAPQ value for unique mappers" - help="STAR bases the mapping quality scores of alignment records in its BAM output on the number of alternative mappings for the read. If a read maps to multiple locations on the reference genome, the following MAPQ scoring scheme is -used: >=5 mappings => MAPQ=0; 3-4 mappings => MAPQ=1; 2 mappings => MAPQ=3. This setting lets you control the MAPQ used for reads mapped to a single location. Set to 255 for compatibility with Cufflink (default in STAR) but keep to 60 for modern downstream tools like mutect2." /> + <param argument="--outSAMmapqUnique" type="integer" value="60" min="0" max="255" label="MAPQ value for unique mappers" help="STAR bases the mapping quality scores of alignment records in its BAM output on the number of alternative mappings for the read. If a read maps to multiple locations on the reference genome, the following MAPQ scoring scheme is used: >=5 mappings => MAPQ=0; 3-4 mappings => MAPQ=1; 2 mappings => MAPQ=3. This setting lets you control the MAPQ used for reads mapped to a single location. Set to 255 for compatibility with Cufflink (default in STAR) but keep to 60 for modern downstream tools like mutect2."/> + </xml> + <xml name="wasp"> + <!-- + This is re-implementation of the original WASP algorithm by Bryce van de Geijn, Graham McVicker, + Yoav Gilad and Jonathan K Pritchard. Please cite the original WASP paper: Nature Methods 12, + 1061–1063 (2015) https://www.nature.com/articles/nmeth.3582. WASP filtering is activated + with "waspOutputMode SAMtag". + --> + <conditional name="wasp_conditional"> + <param argument="--waspOutputMode" type="select" label="Actiavte WASP filtering"> + <help><![CDATA[This is a reimplementation of the original WASP algorithm by Bryce van de Geijn, Graham McVicker, + Yoav Gilad and Jonathan K Pritchard. https://doi.org/10.1038/nmeth.3582. This option will add the vW tag to the SAM output. vW:i:1 means + alignment passed WASP filtering, and all other values mean it did not:<br/> + - vW:i:2 = multi-mapping read<br/> + - vW:i:3 = variant base in the read is N (non-ACGT)<br/> + - vW:i:4 = remapped read did not map <br/> + - vW:i:5 = remapped read multi-maps <br/> + - vW:i:6 = remapped read maps to a different locus <br/> + - vW:i:7 = read overlaps too many variants <br/> + ]]> + </help> + <option value="" selected="true">No WASP filtering</option> + <option value="wasp_mode">Activate WASP filtering</option> + </param> + <when value="wasp_mode"> + <param argument="--varVCFfile" type="data" format="vcf" label="VCF file with personal variants" help="Each variant is expected to have a genotype with two alleles. The VCF file needs to have the 10th column with genotype recorded as 0/1, 1/0, 1/1 (or | instead of /)"/> + </when> + <when value=""/> + </conditional> </xml> </macros>
--- a/rg_rnaStarSolo.xml Wed Feb 14 09:04:09 2024 +0000 +++ b/rg_rnaStarSolo.xml Tue Aug 27 14:11:53 2024 +0000 @@ -94,6 +94,11 @@ --soloCBwhitelist None #end if + #if $solo.wasp_conditional.waspOutputMode == "wasp_mode": + --waspOutputMode SAMtag + --varVCFfile '$solo.wasp_conditional.varVCFfile' + #end if + --soloStrand $solo.soloStrand --soloFeatures $solo.soloFeatures --soloUMIdedup $sc.umidedup.soloUMIdedup @@ -355,6 +360,7 @@ <option value="GeneFull_Ex50pAS" >Full: Count all reads overlapping genes' exons and introns: prioritize 50% overlap with exons. Do not count reads with 100% exonic overlap in the antisense direction.</option> <option value="Gene Velocyto">Velocyto: calculate spliced, unspliced, and ambiguous counts per cell per gene similar to the velocyto tool</option> </param> + <expand macro="wasp"/> <conditional name="filter" > <param name="filter_type" type="select" label="Cell filtering type and parameters" > <option value="cellranger2" selected="true" >Simple filtering of CellRanger v2</option> @@ -515,6 +521,10 @@ <param name="soloStrand" value="Forward" /> <param name="soloFeatures" value="Gene" /> <param name="quantModeGene" value="true" /> + <conditional name="wasp_conditional"> + <param name="waspOutputMode" value="wasp_mode"/> + <param name="varVCFfile" value="filtered3.vcf" ftype="vcf" /> + </conditional> </section> <output name="output_barcodes" > <assert_contents> @@ -544,7 +554,7 @@ <has_line_matching expression="\s+yesUMIs\s+8" /> </assert_contents> </output> - <output name="output_BAM" value="filtered3.bam" compare="sim_size" delta="600" /> + <output name="output_BAM" value="filtered4.bam" ftype="bam" lines_diff="6"/> <output name="reads_per_gene" > <assert_contents> <has_line_matching expression="ENSG00000279493\s+0\s+0\s+0" />
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtered3.vcf Tue Aug 27 14:11:53 2024 +0000 @@ -0,0 +1,175 @@ +##fileformat=VCFv4.2 +##FILTER=<ID=PASS,Description="All filters passed"> +##bcftoolsVersion=1.15.1+htslib-1.15.1 +##bcftoolsCommand=mpileup -f filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa filtered3.bam +##reference=file://filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa +##contig=<ID=21,length=697740> +##ALT=<ID=*,Description="Represents allele(s) other than observed."> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> +##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of raw reads supporting an indel"> +##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of raw reads supporting an indel"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> +##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3"> +##INFO=<ID=RPBZ,Number=1,Type=Float,Description="Mann-Whitney U-z test of Read Position Bias (closer to 0 is better)"> +##INFO=<ID=MQBZ,Number=1,Type=Float,Description="Mann-Whitney U-z test of Mapping Quality Bias (closer to 0 is better)"> +##INFO=<ID=BQBZ,Number=1,Type=Float,Description="Mann-Whitney U-z test of Base Quality Bias (closer to 0 is better)"> +##INFO=<ID=MQSBZ,Number=1,Type=Float,Description="Mann-Whitney U-z test of Mapping Quality vs Strand Bias (closer to 0 is better)"> +##INFO=<ID=SCBZ,Number=1,Type=Float,Description="Mann-Whitney U-z test of Soft-Clip Length Bias (closer to 0 is better)"> +##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> +##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric."> +##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)"> +##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> +##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases"> +##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality"> +##bcftools_callVersion=1.15.1+htslib-1.15.1 +##bcftools_callCommand=call -mv -Ob -o filtered3.bcf; Date=Tue Aug 27 14:09:53 2024 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT filtered3.bam +21 13871 . G A 8.19139 . DP=16;VDB=0.163924;SGB=-0.651104;RPBZ=-1.26304;MQBZ=1.7272;BQBZ=1;SCBZ=-0.447396;FS=0;MQ0F=0.0625;AC=1;AN=2;DP4=8,0,8,0;MQ=9 GT:PL 0/1:38,0,6 +21 13918 . A G 8.05611 . DP=9;VDB=0.12166;SGB=-0.616816;RPBZ=1.03713;MQBZ=-0.154303;BQBZ=0;SCBZ=0.707107;FS=0;MQ0F=0.111111;AC=1;AN=2;DP4=3,0,6,0;MQ=14 GT:PL 0/1:40,0,15 +21 13924 . G A 27.0767 . DP=11;VDB=0.0108096;SGB=-0.651104;RPBZ=-0.261911;MQBZ=0.968246;BQBZ=-0.745356;SCBZ=-0.931695;FS=0;MQ0F=0.0909091;AC=2;AN=2;DP4=2,0,8,0;MQ=14 GT:PL 1/1:54,3,0 +21 13928 . G C 34.42 . DP=11;VDB=0.0257451;SGB=-0.670168;FS=0;MQ0F=0.0909091;AC=2;AN=2;DP4=0,0,10,0;MQ=14 GT:PL 1/1:64,24,0 +21 13962 . A G 3.21856 . DP=13;VDB=0.00595258;SGB=-0.616816;RPBZ=2.14581;MQBZ=0.245201;BQBZ=-0.113961;SCBZ=-1.73888;FS=0;MQ0F=0.0769231;AC=1;AN=2;DP4=7,0,6,0;MQ=12 GT:PL 0/1:33,0,34 +21 15349 . G C 3.74242 . DP=33;VDB=3.28209e-07;SGB=-0.689466;RPBZ=-1.0584;MQBZ=1.31911;MQSBZ=-1.01601;BQBZ=-1.40181;SCBZ=0.601646;FS=0;MQ0F=0.0606061;AC=1;AN=2;DP4=1,15,1,15;MQ=13 GT:PL 0/1:34,0,49 +21 15425 . T C 15.3182 . DP=21;VDB=0.739317;SGB=-0.686358;RPBZ=-1.79168;MQBZ=0.125524;BQBZ=1.41022;SCBZ=0.514874;FS=0;MQ0F=0;AC=1;AN=2;DP4=0,7,0,14;MQ=12 GT:PL 0/1:47,0,9 +21 15431 . G A 6.81655 . DP=18;VDB=0.777008;SGB=-0.683931;RPBZ=-0.93741;MQBZ=-1.01859;BQBZ=1.61245;SCBZ=-1.53815;FS=0;MQ0F=0;AC=1;AN=2;DP4=0,5,0,13;MQ=10 GT:PL 0/1:38,0,11 +21 19605 . A G 7.20516 . DP=9;VDB=0.534935;SGB=-0.590765;RPBZ=0.489898;MQBZ=0.169031;MQSBZ=-0.534522;BQBZ=0.33541;SCBZ=-0.873128;FS=0;MQ0F=0;AC=1;AN=2;DP4=1,3,0,5;MQ=16 GT:PL 0/1:39,0,26 +21 19637 . A G 12.9958 . DP=5;VDB=0.360777;SGB=-0.556411;RPBZ=-0.707107;MQBZ=-0.5;MQSBZ=-0.5;BQBZ=-0.5;SCBZ=0.5;FS=0;MQ0F=0;AC=1;AN=2;DP4=0,1,1,3;MQ=16 GT:PL 0/1:43,0,5 +21 19654 . C T 4.85359 . DP=4;VDB=0.18;SGB=-0.453602;RPBZ=-1.54919;MQBZ=1.63299;MQSBZ=-0.942809;BQBZ=0;SCBZ=1;FS=0;MQ0F=0.25;AC=2;AN=2;DP4=0,2,1,1;MQ=10 GT:PL 1/1:30,2,0 +21 19742 . T C 7.30814 . DP=2;VDB=0.36;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,0,2;MQ=20 GT:PL 1/1:36,6,0 +21 19744 . A G 7.30814 . DP=2;VDB=0.32;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,0,2;MQ=20 GT:PL 1/1:36,6,0 +21 19811 . T C 8.50643 . DP=10;VDB=0.0411825;SGB=-0.616816;RPBZ=-0.427699;MQBZ=1.71761;BQBZ=0;SCBZ=-0.731925;FS=0;MQ0F=0.2;AC=1;AN=2;DP4=4,0,6,0;MQ=10 GT:PL 0/1:38,0,5 +21 19866 . A C 37.4152 . DP=6;VDB=0.168702;SGB=-0.616816;FS=0;MQ0F=0.166667;AC=2;AN=2;DP4=0,0,6,0;MQ=16 GT:PL 1/1:67,18,0 +21 19881 . T C 19.4636 . DP=4;VDB=0.784982;SGB=-0.556411;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,4,0;MQ=15 GT:PL 1/1:49,12,0 +21 20703 . A G 6.0118 . DP=15;VDB=0.000802463;SGB=-0.680642;RPBZ=1.37489;MQBZ=-0.787761;BQBZ=2;SCBZ=0;FS=0;MQ0F=0.133333;AC=1;AN=2;DP4=3,0,12,0;MQ=11 GT:PL 0/1:33,0,2 +21 20716 . A G 21.9575 . DP=21;VDB=0.0812721;SGB=-0.69168;RPBZ=1.56004;MQBZ=-0.254328;BQBZ=-0.470162;SCBZ=-0.806322;FS=0;MQ0F=0.0952381;AC=2;AN=2;DP4=2,0,19,0;MQ=8 GT:PL 1/1:49,30,0 +21 27426 . G C 14.5766 . DP=6;VDB=0.0411825;SGB=-0.616816;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,0,6;MQ=14 GT:PL 1/1:46,17,2 +21 27432 . G T 18.4764 . DP=6;VDB=0.0389458;SGB=-0.616816;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,0,6;MQ=14 GT:PL 1/1:48,18,0 +21 27882 . A G 4.4843 . DP=17;VDB=0.696154;SGB=-0.680642;RPBZ=-1.21295;MQBZ=-0.0564227;MQSBZ=0.983359;BQBZ=-0.645497;SCBZ=-2.26608;FS=0;MQ0F=0.0588235;AC=1;AN=2;DP4=4,1,12,0;MQ=10 GT:PL 0/1:34,0,8 +21 27933 . A G 21.3683 . DP=25;VDB=0.347065;SGB=-0.686358;RPBZ=0.848872;MQBZ=0.0622633;MQSBZ=0.7886;BQBZ=0.428896;SCBZ=-1.60703;FS=0;MQ0F=0.04;AC=1;AN=2;DP4=11,0,13,1;MQ=12 GT:PL 0/1:54,0,33 +21 27958 . T C 12.0816 . DP=10;VDB=0.316575;SGB=-0.651104;RPBZ=0.783349;MQBZ=-0.75;BQBZ=-0.5;SCBZ=0.5;FS=0;MQ0F=0;AC=1;AN=2;DP4=2,0,8,0;MQ=16 GT:PL 0/1:44,0,10 +21 27990 . T C 17.3194 . DP=4;VDB=0.309755;SGB=-0.511536;RPBZ=1.34164;MQBZ=1.73205;BQBZ=-0.57735;SCBZ=0.942809;FS=0;MQ0F=0;AC=2;AN=2;DP4=1,0,3,0;MQ=15 GT:PL 1/1:44,5,0 +21 28137 . G C 19.4636 . DP=4;VDB=0.131345;SGB=-0.556411;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,4,0;MQ=15 GT:PL 1/1:49,12,0 +21 29792 . C T 7.27325 . DP=7;VDB=0.0221621;SGB=-0.556411;RPBZ=0.180021;MQBZ=0.440959;MQSBZ=0;BQBZ=0;SCBZ=2.2014;FS=0;MQ0F=0;AC=1;AN=2;DP4=3,0,1,3;MQ=14 GT:PL 0/1:39,0,20 +21 29810 . G A 77.4149 . DP=24;VDB=1.25119e-06;SGB=-0.692717;MQSBZ=0.524975;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,20,3;MQ=12 GT:PL 1/1:107,69,0 +21 29842 . C T 21.1507 . DP=47;VDB=0.0659263;SGB=-0.691153;RPBZ=0.0328523;MQBZ=0.41088;MQSBZ=0.598526;BQBZ=0.787839;SCBZ=2.34163;FS=0;MQ0F=0.0212766;AC=1;AN=2;DP4=26,3,15,3;MQ=13 GT:PL 0/1:54,0,56 +21 29908 . T C 42.9541 . DP=16;VDB=0.00415584;SGB=-0.683931;RPBZ=0.373337;MQBZ=-0.829774;MQSBZ=0.203566;BQBZ=-0.407039;SCBZ=0.517769;FS=0;MQ0F=0.0625;AC=2;AN=2;DP4=1,0,11,2;MQ=12 GT:PL 1/1:70,19,0 +21 29919 . A G 19.2592 . DP=6;VDB=0.0414745;SGB=-0.590765;RPBZ=1.48522;MQBZ=0.933257;MQSBZ=-0.311086;BQBZ=-0.948683;SCBZ=0.447214;FS=0;MQ0F=0.166667;AC=2;AN=2;DP4=1,0,4,1;MQ=10 GT:PL 1/1:46,10,0 +21 30209 . G A 7.30814 . DP=2;VDB=0.1;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,2,0;MQ=20 GT:PL 1/1:36,6,0 +21 30213 . G A 7.30814 . DP=2;VDB=0.1;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,2,0;MQ=20 GT:PL 1/1:36,6,0 +21 35166 . G A 8.08613 . DP=32;VDB=0.000100416;SGB=-0.692067;RPBZ=2.35842;MQBZ=0.0865916;BQBZ=0.324617;SCBZ=1.38514;FS=0;MQ0F=0.0625;AC=1;AN=2;DP4=0,12,0,20;MQ=11 GT:PL 0/1:40,0,33 +21 35229 . G C 24.4377 . DP=19;VDB=0.220127;SGB=-0.69168;MQSBZ=0.682959;FS=0;MQ0F=0.105263;AC=2;AN=2;DP4=0,0,1,18;MQ=8 GT:PL 1/1:54,48,0 +21 35243 . A C 38.9535 . DP=19;VDB=0.18357;SGB=-0.690438;RPBZ=1.33076;MQBZ=0.500703;MQSBZ=0.884764;BQBZ=-0.342997;SCBZ=0.85812;FS=0;MQ0F=0.105263;AC=2;AN=2;DP4=0,2,1,16;MQ=10 GT:PL 1/1:66,27,0 +21 35301 . C T 3.22451 . DP=4;VDB=0.0681597;SGB=-0.511536;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,0,3;MQ=14 GT:PL 1/1:30,9,0 +21 36052 . C A 21.4492 . DP=13;VDB=0.0262535;SGB=-0.680642;MQSBZ=-1.68732;FS=0;MQ0F=0.0769231;AC=2;AN=2;DP4=0,0,11,1;MQ=9 GT:PL 1/1:51,33,0 +21 36053 . A G 5.97965 . DP=13;VDB=0.0258627;SGB=-0.676189;RPBZ=-1.01567;MQBZ=-1.07375;MQSBZ=-1.68732;BQBZ=-0.445362;SCBZ=-1.21854;FS=0;MQ0F=0.0769231;AC=2;AN=2;DP4=1,0,10,1;MQ=9 GT:PL 1/1:32,13,0 +21 37577 . A G 6.30333 . DP=5;VDB=0.0452455;SGB=-0.556411;RPBZ=1.11803;MQBZ=0.372678;MQSBZ=-0.372678;BQBZ=-0.5;SCBZ=1.11803;FS=0;MQ0F=0.2;AC=2;AN=2;DP4=0,1,4,0;MQ=9 GT:PL 1/1:32,8,0 +21 37653 . A G 44.4192 . DP=13;VDB=0.00955183;SGB=-0.683931;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,13,0;MQ=13 GT:PL 1/1:74,36,0 +21 37658 . G C 36.4192 . DP=15;VDB=0.0373922;SGB=-0.688148;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,15,0;MQ=11 GT:PL 1/1:66,42,0 +21 37661 . A G 5.7493 . DP=16;VDB=0.126837;SGB=-0.636426;RPBZ=0.741504;MQBZ=0.722806;BQBZ=0.311046;SCBZ=-0.452414;FS=0;MQ0F=0;AC=1;AN=2;DP4=9,0,7,0;MQ=12 GT:PL 0/1:37,0,29 +21 37706 . C G 6.82671 . DP=12;VDB=0.0572236;SGB=-0.680642;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,12,0;MQ=11 GT:PL 1/1:50,39,15 +21 37778 . A G 8.13869 . DP=3;VDB=0.0560361;SGB=-0.511536;FS=0;MQ0F=0.333333;AC=2;AN=2;DP4=0,0,3,0;MQ=13 GT:PL 1/1:37,9,0 +21 38899 . G A 5.61693 . DP=3;VDB=0.26;SGB=-0.453602;RPBZ=-1.22474;MQBZ=1.41421;BQBZ=-0.707107;SCBZ=0.707107;FS=0;MQ0F=0.333333;AC=2;AN=2;DP4=0,1,0,2;MQ=13 GT:PL 1/1:31,3,0 +21 38910 . A G 8.13869 . DP=3;VDB=0.185719;SGB=-0.511536;FS=0;MQ0F=0.333333;AC=2;AN=2;DP4=0,0,0,3;MQ=13 GT:PL 1/1:37,9,0 +21 38941 . T C 35.0072 . DP=10;VDB=0.49524;SGB=-0.651104;RPBZ=1.1786;MQBZ=0.968246;BQBZ=1.30437;SCBZ=-0.963794;FS=0;MQ0F=0.1;AC=2;AN=2;DP4=0,2,0,8;MQ=14 GT:PL 1/1:62,11,0 +21 45996 . A G 10.5539 . DP=7;VDB=0.0452455;SGB=-0.556411;RPBZ=-0.178377;MQBZ=1.1547;BQBZ=1.1547;SCBZ=-0.540062;FS=0;MQ0F=0;AC=1;AN=2;DP4=3,0,4,0;MQ=17 GT:PL 0/1:43,0,20 +21 46012 . G A 17.1077 . DP=9;VDB=0.00467508;SGB=-0.636426;RPBZ=-0.29277;MQBZ=-0.808122;BQBZ=1.87083;SCBZ=-0.46291;FS=0;MQ0F=0;AC=1;AN=2;DP4=2,0,7,0;MQ=15 GT:PL 0/1:46,0,3 +21 46016 . A G 21.2626 . DP=10;VDB=0.0987508;SGB=-0.651104;RPBZ=-0.783349;MQBZ=1.125;BQBZ=-0.5;SCBZ=-0.140242;FS=0;MQ0F=0;AC=2;AN=2;DP4=2,0,8,0;MQ=16 GT:PL 1/1:48,1,0 +21 46027 . A G 15.309 . DP=20;VDB=0.0607471;SGB=-0.676189;RPBZ=-0.152119;MQBZ=1.12615;BQBZ=-0.549946;SCBZ=-2.65745;FS=0;MQ0F=0.05;AC=1;AN=2;DP4=9,0,11,0;MQ=12 GT:PL 0/1:48,0,26 +21 46130 . A G 10.7632 . DP=13;VDB=0.0760875;SGB=-0.651104;RPBZ=0.659639;MQBZ=-0.401112;MQSBZ=0.741063;BQBZ=-0.790569;SCBZ=1.16775;FS=0;MQ0F=0.0769231;AC=1;AN=2;DP4=5,0,5,3;MQ=11 GT:PL 0/1:43,0,24 +21 46817 . A G 5.74887 . DP=17;VDB=0.342281;SGB=-0.662043;RPBZ=0.289385;MQBZ=-0.487798;BQBZ=0;SCBZ=0.129433;FS=0;MQ0F=0.176471;AC=1;AN=2;DP4=0,8,0,9;MQ=12 GT:PL 0/1:37,0,37 +21 46824 . A G 5.74887 . DP=17;VDB=0.00667786;SGB=-0.662043;RPBZ=0.723909;MQBZ=-0.704597;BQBZ=0;SCBZ=0.905028;FS=0;MQ0F=0.176471;AC=1;AN=2;DP4=0,8,0,9;MQ=12 GT:PL 0/1:37,0,37 +21 46827 . C T 5.03467 . DP=16;VDB=0.00487534;SGB=-0.636426;RPBZ=-0.26541;MQBZ=0.612938;BQBZ=0;SCBZ=-1.04295;FS=0;MQ0F=0.1875;AC=1;AN=2;DP4=0,9,0,7;MQ=13 GT:PL 0/1:36,0,38 +21 46868 . G A 19.4636 . DP=5;VDB=0.857144;SGB=-0.511536;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,0,3;MQ=20 GT:PL 1/1:49,9,0 +21 50245 . T A 27.4222 . DP=8;VDB=0.163924;SGB=-0.651104;FS=0;MQ0F=0.25;AC=2;AN=2;DP4=0,0,8,0;MQ=12 GT:PL 1/1:57,24,0 +21 50266 . A G 27.2551 . DP=6;VDB=0.110342;SGB=-0.590765;RPBZ=0.29277;MQBZ=1.41421;BQBZ=-0.447214;SCBZ=0;FS=0;MQ0F=0.333333;AC=2;AN=2;DP4=1,0,5,0;MQ=13 GT:PL 1/1:54,10,0 +21 50269 . G C 4.15607 . DP=6;VDB=0.0433485;SGB=-0.511536;RPBZ=1.96396;MQBZ=1.58114;BQBZ=1;SCBZ=0;FS=0;MQ0F=0.333333;AC=1;AN=2;DP4=3,0,3,0;MQ=13 GT:PL 0/1:34,0,10 +21 50270 . C G 9.02432 . DP=7;VDB=0.084975;SGB=-0.636426;FS=0;MQ0F=0.285714;AC=2;AN=2;DP4=0,0,7,0;MQ=11 GT:PL 1/1:46,20,8 +21 50661 . G A 7.30814 . DP=2;VDB=0.1;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,2,0;MQ=20 GT:PL 1/1:36,6,0 +21 50704 . A C 8.13869 . DP=3;VDB=0.364077;SGB=-0.511536;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,3,0;MQ=14 GT:PL 1/1:37,9,0 +21 51204 . C G 15.5259 . DP=36;VDB=0.000362184;SGB=-0.69168;RPBZ=-0.625851;MQBZ=0.0864411;MQSBZ=1.20664;BQBZ=0;SCBZ=0;FS=0;MQ0F=0.0277778;AC=1;AN=2;DP4=1,14,0,19;MQ=14 GT:PL 0/1:48,0,47 +21 51287 . T C 11.9325 . DP=32;VDB=0.0211251;SGB=-0.692831;RPBZ=0.217737;MQBZ=-1.188;MQSBZ=-0.25502;BQBZ=-1.37823;SCBZ=-2.27742;FS=0;MQ0F=0;AC=1;AN=2;DP4=1,7,1,23;MQ=11 GT:PL 0/1:43,0,8 +21 51868 . A T 35.0172 . DP=22;VDB=0.00829484;SGB=-0.692067;RPBZ=0.685829;MQBZ=-0.196214;MQSBZ=-1.35401;BQBZ=2.06216;SCBZ=-1.9261;FS=0;MQ0F=0;AC=2;AN=2;DP4=2,0,19,1;MQ=12 GT:PL 1/1:62,28,0 +21 51917 . C T 10.873 . DP=22;VDB=0.0282545;SGB=-0.689466;RPBZ=-1.10613;MQBZ=0.957427;BQBZ=-1.11155;SCBZ=1.50667;FS=0;MQ0F=0;AC=2;AN=2;DP4=6,0,16,0;MQ=10 GT:PL 1/1:38,0,1 +21 52178 . T C 6.00737 . DP=13;VDB=0.0909239;SGB=-0.662043;RPBZ=-1.15887;MQBZ=-0.165087;BQBZ=2.20794;SCBZ=0.882823;FS=0;MQ0F=0.0769231;AC=1;AN=2;DP4=4,0,9,0;MQ=10 GT:PL 0/1:33,0,2 +21 52221 . G A 11.7419 . DP=5;VDB=0.409395;SGB=-0.590765;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,5,0;MQ=16 GT:PL 1/1:50,18,9 +21 52329 . G A 6.32811 . DP=4;VDB=0.529687;SGB=-0.511536;RPBZ=-1.34164;MQBZ=1.41421;BQBZ=0;SCBZ=-1.73205;FS=0;MQ0F=0.25;AC=2;AN=2;DP4=1,0,3,0;MQ=10 GT:PL 1/1:32,5,0 +21 60392 . T C 3.64636 . DP=9;VDB=0.314313;SGB=-0.556411;RPBZ=-0.734847;MQBZ=-1.11803;MQSBZ=-0.353553;BQBZ=0;SCBZ=-1.34164;FS=0;MQ0F=0;AC=1;AN=2;DP4=0,5,1,3;MQ=18 GT:PL 0/1:34,0,48 +21 60396 . G A 6.50182 . DP=9;VDB=0.372756;SGB=-0.556411;RPBZ=0;MQBZ=0.894427;MQSBZ=-0.353553;BQBZ=-1.11803;SCBZ=0.33541;FS=0;MQ0F=0;AC=1;AN=2;DP4=1,4,0,4;MQ=18 GT:PL 0/1:38,0,48 +21 60419 . A G 3.72363 . DP=9;VDB=0.0645318;SGB=-0.556411;RPBZ=1.85262;MQBZ=0;MQSBZ=-0.53033;BQBZ=0;SCBZ=-1.34164;FS=0;MQ0F=0;AC=1;AN=2;DP4=0,5,1,3;MQ=16 GT:PL 0/1:34,0,40 +21 60770 . A C 47.3472 . DP=18;VDB=0.662143;SGB=-0.690438;RPBZ=1.44635;MQBZ=1.73462;MQSBZ=1.15641;BQBZ=-0.352941;SCBZ=-1.73506;FS=0;MQ0F=0.0555556;AC=2;AN=2;DP4=0,1,1,16;MQ=14 GT:PL 1/1:74,33,0 +21 60813 . T C 8.10157 . DP=15;VDB=0.0663569;SGB=-0.651104;RPBZ=0.290097;MQBZ=0.395285;BQBZ=-0.935414;SCBZ=-1.56492;FS=0;MQ0F=0;AC=1;AN=2;DP4=0,7,0,8;MQ=12 GT:PL 0/1:40,0,31 +21 60850 . T C 8.13869 . DP=3;VDB=0.756524;SGB=-0.511536;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,0,3;MQ=13 GT:PL 1/1:37,9,0 +21 62454 . A T 25.9268 . DP=11;VDB=0.115319;SGB=-0.670168;RPBZ=-0.948683;MQBZ=-0.737028;BQBZ=-0.316228;SCBZ=0.471405;FS=0;MQ0F=0.181818;AC=2;AN=2;DP4=1,0,10,0;MQ=12 GT:PL 1/1:53,10,0 +21 62491 . T C 11.4795 . DP=16;VDB=0.266813;SGB=-0.676189;RPBZ=1.81528;MQBZ=0.524802;BQBZ=0.492366;SCBZ=0.183211;FS=0;MQ0F=0;AC=1;AN=2;DP4=5,0,11,0;MQ=13 GT:PL 0/1:44,0,19 +21 62492 . G A 13.4162 . DP=15;VDB=0.289496;SGB=-0.651104;RPBZ=1.79699;MQBZ=1.59476;BQBZ=-0.935414;SCBZ=0.122597;FS=0;MQ0F=0;AC=1;AN=2;DP4=7,0,8,0;MQ=13 GT:PL 0/1:46,0,23 +21 62535 . T C 12.5601 . DP=11;VDB=0.173752;SGB=-0.636426;RPBZ=-1.13648;MQBZ=-1.12122;BQBZ=0;SCBZ=-0.38503;FS=0;MQ0F=0;AC=1;AN=2;DP4=4,0,7,0;MQ=16 GT:PL 0/1:45,0,33 +21 62935 . A G 6.45586 . DP=36;VDB=0.00893984;SGB=-0.692831;RPBZ=-0.553846;MQBZ=-0.407841;MQSBZ=-1.67857;BQBZ=0.5073;SCBZ=1.00855;FS=0;MQ0F=0.0833333;AC=1;AN=2;DP4=12,0,23,1;MQ=9 GT:PL 0/1:38,0,15 +21 62981 . T G 8.13869 . DP=3;VDB=0.0349627;SGB=-0.511536;FS=0;MQ0F=0.333333;AC=2;AN=2;DP4=0,0,3,0;MQ=13 GT:PL 1/1:37,9,0 +21 62984 . A G 6.32811 . DP=4;VDB=0.0349627;SGB=-0.511536;RPBZ=1.34164;MQBZ=0.471405;BQBZ=0;SCBZ=-1.73205;FS=0;MQ0F=0.25;AC=2;AN=2;DP4=1,0,3,0;MQ=10 GT:PL 1/1:32,5,0 +21 63080 . T G 26.4242 . DP=5;VDB=0.197286;SGB=-0.590765;MQSBZ=0.790569;FS=0;MQ0F=0.2;AC=2;AN=2;DP4=0,0,4,1;MQ=12 GT:PL 1/1:56,15,0 +21 70129 . A G 7.30814 . DP=2;VDB=0.28;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,0,2;MQ=20 GT:PL 1/1:36,6,0 +21 70231 . C T 7.30814 . DP=3;VDB=0.06;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,0,2;MQ=20 GT:PL 1/1:36,6,0 +21 70232 . G A 5.61693 . DP=3;VDB=0.06;SGB=-0.453602;RPBZ=1.22474;MQBZ=1.41421;BQBZ=1.41421;SCBZ=0;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,1,0,2;MQ=13 GT:PL 1/1:31,3,0 +21 74439 . A G 19.4636 . DP=3;VDB=0.336489;SGB=-0.511536;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,3,0;MQ=20 GT:PL 1/1:49,9,0 +21 74453 . T A 8.13869 . DP=3;VDB=0.345596;SGB=-0.511536;FS=0;MQ0F=0.333333;AC=2;AN=2;DP4=0,0,3,0;MQ=13 GT:PL 1/1:37,9,0 +21 75748 . G A 31.8678 . DP=11;VDB=0.382624;SGB=-0.670168;RPBZ=0.948683;MQBZ=-0.74162;MQSBZ=1.85405;BQBZ=-0.469042;SCBZ=0.469042;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,1,1,9;MQ=13 GT:PL 1/1:59,13,0 +21 75756 . A G 31.2817 . DP=9;VDB=0.77747;SGB=-0.651104;RPBZ=0;MQBZ=1.41421;BQBZ=-0.353553;SCBZ=-2.12132;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,1,0,8;MQ=14 GT:PL 1/1:58,15,0 +21 75806 . A G 3.73811 . DP=13;VDB=0.0760875;SGB=-0.651104;RPBZ=-0.659639;MQBZ=-0.802225;BQBZ=1.26491;SCBZ=0.0775791;FS=0;MQ0F=0.0769231;AC=1;AN=2;DP4=0,5,0,8;MQ=11 GT:PL 0/1:34,0,22 +21 75821 . T C 16.3508 . DP=11;VDB=0.00114085;SGB=-0.670168;RPBZ=-0.953025;MQBZ=0.335888;BQBZ=-0.469042;SCBZ=1.00509;FS=0;MQ0F=0.0909091;AC=2;AN=2;DP4=0,1,0,10;MQ=10 GT:PL 1/1:43,20,0 +21 81337 . C T 5.00423 . DP=11;VDB=0.0224626;SGB=-0.590765;RPBZ=-1.27802;MQBZ=0;BQBZ=0;SCBZ=-1.74801;FS=0;MQ0F=0;AC=1;AN=2;DP4=6,0,5,0;MQ=16 GT:PL 0/1:36,0,45 +21 81342 . C G 19.0687 . DP=11;VDB=0.00262538;SGB=-0.670168;RPBZ=0.633898;MQBZ=-0.469042;BQBZ=-0.316228;SCBZ=-1.63299;FS=0;MQ0F=0;AC=2;AN=2;DP4=1,0,10,0;MQ=16 GT:PL 1/1:58,17,12 +21 81349 . C T 3.77891 . DP=12;VDB=0.0525422;SGB=-0.590765;RPBZ=-0.893198;MQBZ=1.37017;BQBZ=0.845154;SCBZ=-1.60357;FS=0;MQ0F=0.0833333;AC=1;AN=2;DP4=7,0,5,0;MQ=12 GT:PL 0/1:34,0,26 +21 81441 . A C 28.4205 . DP=6;VDB=0.072067;SGB=-0.616816;FS=0;MQ0F=0.166667;AC=2;AN=2;DP4=0,0,6,0;MQ=13 GT:PL 1/1:58,18,0 +21 81447 . G A 19.4636 . DP=3;VDB=0.0506481;SGB=-0.511536;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,3,0;MQ=20 GT:PL 1/1:49,9,0 +21 88097 . G T 43.0532 . DP=15;VDB=0.441271;SGB=-0.683931;RPBZ=-0.511815;MQBZ=0.0969111;MQSBZ=0.792406;BQBZ=1.21626;SCBZ=1.46152;FS=0;MQ0F=0.0666667;AC=2;AN=2;DP4=2,0,12,1;MQ=12 GT:PL 1/1:70,19,0 +21 88111 . A G 23.2308 . DP=7;VDB=0.530999;SGB=-0.616816;RPBZ=0;MQBZ=-0.62361;MQSBZ=0.62361;BQBZ=-0.408248;SCBZ=-0.264575;FS=0;MQ0F=0;AC=2;AN=2;DP4=1,0,5,1;MQ=14 GT:PL 1/1:50,1,0 +21 88160 . C G 6.76147 . DP=11;VDB=0.0298868;SGB=-0.670168;RPBZ=0.316949;MQBZ=0.520088;MQSBZ=0.866814;BQBZ=-0.316228;SCBZ=0.469042;FS=0;MQ0F=0.181818;AC=2;AN=2;DP4=1,0,9,1;MQ=11 GT:PL 1/1:48,24,16 +21 88202 . A G 7.26048 . DP=4;VDB=0.732596;SGB=-0.511536;RPBZ=-1.34164;MQBZ=0;BQBZ=0;SCBZ=0.57735;FS=0;MQ0F=0;AC=1;AN=2;DP4=1,0,3,0;MQ=20 GT:PL 0/1:38,0,8 +21 91562 . A G 6.32811 . DP=4;VDB=0.309755;SGB=-0.511536;RPBZ=-1.34164;MQBZ=1;BQBZ=0;SCBZ=0;FS=0;MQ0F=0;AC=2;AN=2;DP4=1,0,3,0;MQ=11 GT:PL 1/1:32,5,0 +21 97579 . T C 7.30814 . DP=2;VDB=0.84;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,0,2;MQ=20 GT:PL 1/1:36,6,0 +21 98696 . C T 3.22451 . DP=5;VDB=0.588406;SGB=-0.590765;FS=0;MQ0F=0.2;AC=2;AN=2;DP4=0,0,5,0;MQ=8 GT:PL 1/1:30,15,0 +21 115868 . A G 26.4242 . DP=8;VDB=0.151;SGB=-0.651104;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,8,0;MQ=11 GT:PL 1/1:56,24,0 +21 117459 . C T 24.4299 . DP=5;VDB=0.226768;SGB=-0.590765;MQSBZ=1.58114;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,1,4;MQ=12 GT:PL 1/1:54,15,0 +21 117482 . A C 5.48067 . DP=13;VDB=0.835187;SGB=-0.680642;RPBZ=-0.267999;MQBZ=-0.887625;MQSBZ=1.62731;BQBZ=-0.288675;SCBZ=0.288675;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,1,1,11;MQ=11 GT:PL 1/1:40,12,9 +21 117530 . T A 26.3052 . DP=14;VDB=0.0614523;SGB=-0.683931;RPBZ=0.869199;MQBZ=1.18176;BQBZ=1.72091;SCBZ=-1.87083;FS=0;MQ0F=0.0714286;AC=2;AN=2;DP4=0,1,0,13;MQ=9 GT:PL 1/1:53,31,0 +21 117551 . G C 7.30814 . DP=7;VDB=0.0175011;SGB=-0.636426;FS=0;MQ0F=0.142857;AC=2;AN=2;DP4=0,0,0,7;MQ=6 GT:PL 1/1:36,21,0 +21 126011 . C T 5.61693 . DP=3;VDB=0.66;SGB=-0.453602;RPBZ=1.22474;MQBZ=1.41421;BQBZ=0;SCBZ=0;FS=0;MQ0F=0;AC=2;AN=2;DP4=1,0,2,0;MQ=14 GT:PL 1/1:31,3,0 +21 136979 . G A 8.13869 . DP=3;VDB=0.0941127;SGB=-0.511536;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,3,0;MQ=14 GT:PL 1/1:37,9,0 +21 136988 . A G 8.13869 . DP=3;VDB=0.0941127;SGB=-0.511536;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,3,0;MQ=14 GT:PL 1/1:37,9,0 +21 137088 . T C 5.61693 . DP=3;VDB=0.02;SGB=-0.453602;RPBZ=-1.22474;MQBZ=1.41421;BQBZ=0;SCBZ=0;FS=0;MQ0F=0;AC=2;AN=2;DP4=1,0,2,0;MQ=14 GT:PL 1/1:31,3,0 +21 137113 . G A 7.30814 . DP=2;VDB=0.02;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,2,0;MQ=20 GT:PL 1/1:36,6,0 +21 138443 . T G 12.6566 . DP=6;VDB=0.000959055;SGB=-0.616816;MQSBZ=1.20605;FS=0;MQ0F=0.166667;AC=2;AN=2;DP4=0,0,5,1;MQ=7 GT:PL 1/1:42,18,0 +21 139664 . A G 12.3697 . DP=11;VDB=0.025915;SGB=-0.616816;RPBZ=-0.0914953;MQBZ=1.27265;MQSBZ=-0.734763;BQBZ=0;SCBZ=-1.62481;FS=0;MQ0F=0.0909091;AC=1;AN=2;DP4=1,4,0,6;MQ=13 GT:PL 0/1:45,0,18 +21 143593 . C T 9.88514 . DP=3;VDB=0.392388;SGB=-0.511536;MQSBZ=-1.41421;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,2,1;MQ=13 GT:PL 1/1:39,9,0 +21 152544 . T C 10.3436 . DP=9;VDB=0.0196075;SGB=-0.590765;RPBZ=-0.996546;MQBZ=1.36931;BQBZ=0.33541;SCBZ=0.894427;FS=0;MQ0F=0;AC=2;AN=2;DP4=4,0,5,0;MQ=11 GT:PL 1/1:37,3,0 +21 152547 . A G 8.54666 . DP=8;VDB=0.00477428;SGB=-0.636426;RPBZ=0.223607;MQBZ=-0.774597;BQBZ=-0.377964;SCBZ=0.377964;FS=0;MQ0F=0;AC=2;AN=2;DP4=1,0,7,0;MQ=12 GT:PL 1/1:35,4,0 +21 221789 . T C 19.4636 . DP=5;VDB=0.300397;SGB=-0.590765;FS=0;MQ0F=0.2;AC=2;AN=2;DP4=0,0,5,0;MQ=12 GT:PL 1/1:49,15,0 +21 221824 . A G 17.2912 . DP=5;VDB=0.446842;SGB=-0.556411;RPBZ=0;MQBZ=0.790569;BQBZ=0;SCBZ=0;FS=0;MQ0F=0.2;AC=2;AN=2;DP4=1,0,4,0;MQ=12 GT:PL 1/1:44,8,0 +21 236291 . A G 3.21958 . DP=7;VDB=0.535497;SGB=-0.556411;RPBZ=0.707107;MQBZ=-0.866025;BQBZ=0;SCBZ=-0.585142;FS=0;MQ0F=0;AC=1;AN=2;DP4=0,3,0,4;MQ=17 GT:PL 0/1:33,0,31 +21 236294 . C T 4.32521 . DP=6;VDB=0.176409;SGB=-0.556411;RPBZ=1.38873;MQBZ=-0.707107;BQBZ=0;SCBZ=0.491869;FS=0;MQ0F=0;AC=1;AN=2;DP4=0,2,0,4;MQ=16 GT:PL 0/1:35,0,19 +21 236295 . A G 4.32521 . DP=6;VDB=0.522837;SGB=-0.556411;RPBZ=0;MQBZ=-0.707107;BQBZ=0;SCBZ=-1.47561;FS=0;MQ0F=0;AC=1;AN=2;DP4=0,2,0,4;MQ=16 GT:PL 0/1:35,0,19 +21 236320 . G A 3.20067 . DP=8;VDB=0.220638;SGB=-0.556411;RPBZ=1.76777;MQBZ=0;BQBZ=-0.866025;SCBZ=0.866025;FS=0;MQ0F=0;AC=1;AN=2;DP4=0,3,0,4;MQ=14 GT:PL 0/1:33,0,20 +21 236327 . A G 6.77159 . DP=6;VDB=0.673544;SGB=-0.590765;RPBZ=-0.29277;MQBZ=-0.69282;BQBZ=-0.447214;SCBZ=0.69282;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,1,0,5;MQ=14 GT:PL 1/1:34,0,2 +21 236359 . A T 8.99921 . DP=4;VDB=0.160409;SGB=-0.556411;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,0,4;MQ=11 GT:PL 1/1:38,12,0 +21 248947 . T C 4.85359 . DP=4;VDB=0.38;SGB=-0.453602;RPBZ=-0.774597;MQBZ=1.73205;MQSBZ=-1;BQBZ=0;SCBZ=1;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,2,1,1;MQ=11 GT:PL 1/1:30,2,0 +21 248966 . G A 12.6566 . DP=4;VDB=0.112085;SGB=-0.556411;MQSBZ=-1;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,1,3;MQ=11 GT:PL 1/1:42,12,0 +21 251560 . C T 11.7172 . DP=3;VDB=0.137328;SGB=-0.511536;MQSBZ=0.707107;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,2,1;MQ=14 GT:PL 1/1:41,9,0 +21 289446 . T C 49.4146 . DP=22;VDB=1.4824e-07;SGB=-0.692562;FS=0;MQ0F=0.0454545;AC=2;AN=2;DP4=0,0,22,0;MQ=12 GT:PL 1/1:79,66,0 +21 289481 . T C 3.73429 . DP=48;VDB=0.22406;SGB=-0.692976;RPBZ=0.341551;MQBZ=-1.11595;BQBZ=-1.2128;SCBZ=-1.70538;FS=0;MQ0F=0.0208333;AC=1;AN=2;DP4=22,0,26,0;MQ=11 GT:PL 0/1:34,0,44 +21 289488 . T C 6.50824 . DP=50;VDB=0.518994;SGB=-0.693021;RPBZ=0.545171;MQBZ=-1.485;BQBZ=2.489;SCBZ=-1.74235;FS=0;MQ0F=0.04;AC=1;AN=2;DP4=23,0,27,0;MQ=11 GT:PL 0/1:38,0,40 +21 289520 . A C 21.7432 . DP=41;VDB=4.57336e-05;SGB=-0.69312;RPBZ=-0.393988;MQBZ=0.311388;BQBZ=2.69313;SCBZ=1.10119;FS=0;MQ0F=0.0243902;AC=2;AN=2;DP4=9,0,32,0;MQ=10 GT:PL 1/1:49,21,0 +21 289647 . G A 3.22451 . DP=3;VDB=0.873285;SGB=-0.511536;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,3,0;MQ=14 GT:PL 1/1:30,9,0 +21 339923 . C T 7.30814 . DP=2;VDB=0.56;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,2,0;MQ=20 GT:PL 1/1:36,6,0 +21 355659 . C T 6.32811 . DP=4;VDB=0.868052;SGB=-0.511536;RPBZ=-1.34164;MQBZ=1;BQBZ=0;SCBZ=0;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,1,0,3;MQ=11 GT:PL 1/1:32,5,0 +21 553515 . C G 7.30814 . DP=2;VDB=0.68;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,2,0;MQ=20 GT:PL 1/1:36,6,0 +21 602273 . A C 6.32811 . DP=4;VDB=0.131948;SGB=-0.511536;RPBZ=-1.34164;MQBZ=1;BQBZ=-0.57735;SCBZ=-1.73205;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,1,0,3;MQ=11 GT:PL 1/1:32,5,0 +21 682407 . G T 7.30814 . DP=2;VDB=0.56;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,0,2;MQ=20 GT:PL 1/1:36,6,0 +21 682421 . T G 7.30814 . DP=2;VDB=0.56;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,0,2;MQ=20 GT:PL 1/1:36,6,0 +21 682423 . C G 7.30814 . DP=2;VDB=0.56;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,0,2;MQ=20 GT:PL 1/1:36,6,0 +21 682426 . G A 7.30814 . DP=2;VDB=0.56;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,0,2;MQ=20 GT:PL 1/1:36,6,0 +21 682568 . A G 8.13869 . DP=5;VDB=0.133161;SGB=-0.590765;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,0,5;MQ=9 GT:PL 1/1:37,15,0 +21 694476 . C G 18.4764 . DP=6;VDB=0.0341101;SGB=-0.616816;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,6,0;MQ=11 GT:PL 1/1:48,18,0 +21 694482 . T C 19.4636 . DP=4;VDB=0.131345;SGB=-0.556411;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,4,0;MQ=15 GT:PL 1/1:49,12,0
--- a/test-data/rnastar_test.log Wed Feb 14 09:04:09 2024 +0000 +++ b/test-data/rnastar_test.log Tue Aug 27 14:11:53 2024 +0000 @@ -3,32 +3,35 @@ Finished on | .* Mapping speed, Million of reads per hour | .* - Number of input reads | 100 - Average input read length | 75 + Number of input reads | 15447 + Average input read length | 119 UNIQUE READS: - Uniquely mapped reads number | 99 - Uniquely mapped reads % | 99.00% - Average mapped length | 74.65 - Number of splices: Total | 52 + Uniquely mapped reads number | 150 + Uniquely mapped reads % | 0.97% + Average mapped length | 105.11 + Number of splices: Total | 131 Number of splices: Annotated (sjdb) | 0 - Number of splices: GT/AG | 52 - Number of splices: GC/AG | 0 - Number of splices: AT/AC | 0 - Number of splices: Non-canonical | 0 - Mismatch rate per base, % | 2.00% - Deletion rate per base | 0.00% - Deletion average length | 0.00 - Insertion rate per base | 0.00% - Insertion average length | 0.00 + Number of splices: GT/AG | 100 + Number of splices: GC/AG | 6 + Number of splices: AT/AC | 1 + Number of splices: Non-canonical | 24 + Mismatch rate per base, % | 6.68% + Deletion rate per base | 0.04% + Deletion average length | 1.17 + Insertion rate per base | 0.04% + Insertion average length | 1.50 MULTI-MAPPING READS: - Number of reads mapped to multiple loci | 1 - % of reads mapped to multiple loci | 1.00% - Number of reads mapped to too many loci | 0 - % of reads mapped to too many loci | 0.00% + Number of reads mapped to multiple loci | 451 + % of reads mapped to multiple loci | 2.92% + Number of reads mapped to too many loci | 58 + % of reads mapped to too many loci | 0.38% UNMAPPED READS: + Number of reads unmapped: too many mismatches | 0 % of reads unmapped: too many mismatches | 0.00% - % of reads unmapped: too short | 0.00% - % of reads unmapped: other | 0.00% + Number of reads unmapped: too short | 7912 + % of reads unmapped: too short | 51.22% + Number of reads unmapped: other | 6876 + % of reads unmapped: other | 44.51% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00%
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnastar_test_splicejunctions_wasp.bed Tue Aug 27 14:11:53 2024 +0000 @@ -0,0 +1,193 @@ +21 13873 52149 1 1 0 0 1 12 +21 13882 20712 2 2 0 0 3 28 +21 13882 29808 2 2 0 0 1 28 +21 13882 35980 2 2 0 0 1 26 +21 13882 50180 2 2 0 0 1 19 +21 13887 27728 1 1 0 0 1 21 +21 13887 35985 1 1 0 0 1 15 +21 13887 51866 1 1 0 0 4 40 +21 13887 62408 1 1 0 0 2 24 +21 13887 88031 1 1 0 0 2 40 +21 13887 152470 1 1 0 2 2 40 +21 13894 50193 1 1 0 0 1 24 +21 13907 27883 2 2 0 0 2 45 +21 13976 19932 2 2 0 0 4 41 +21 13976 88119 2 2 0 0 2 33 +21 13976 108267 2 2 0 0 2 33 +21 13991 30873 2 2 0 0 1 18 +21 13991 52131 2 2 0 0 1 18 +21 15394 46773 1 1 0 0 1 39 +21 18885 50205 2 4 0 0 1 35 +21 18949 28120 1 1 0 0 1 26 +21 18953 27816 2 2 0 0 1 16 +21 18953 37719 2 2 0 1 0 34 +21 19001 46120 2 2 0 0 1 17 +21 19001 52299 2 2 0 0 1 17 +21 19001 63039 2 2 0 0 1 17 +21 19533 60698 2 2 0 1 0 44 +21 19658 51267 1 1 0 0 1 45 +21 19737 28120 1 1 0 0 1 16 +21 19826 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