Mercurial > repos > jjohnson > snpsift
diff snpSift_extractFields.xml @ 4:baf6602903e1
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| author | jjohnson |
|---|---|
| date | Wed, 09 Dec 2015 14:03:26 -0500 |
| parents | |
| children | 824f78c0d0df |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpSift_extractFields.xml Wed Dec 09 14:03:26 2015 -0500 @@ -0,0 +1,221 @@ +<tool id="snpSift_extractFields" name="SnpSift Extract Fields" version="@WRAPPER_VERSION@.0"> + <options sanitize="False" /> + <description>from a VCF file inot a tabular file</description> + <macros> + <import>snpSift_macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command><![CDATA[ + cat "$input" + #if $one_effect_per_line: + | \$SNPEFF_JAR_PATH/scripts/vcfEffOnePerLine.pl + #end if + | java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar extractFields + #if $separator: + -s '$separator' + #end if + #if $empty_text: + -e '$empty_text' + #end if + - + #echo ' '.join(['"%s"' % x for x in $extract.split()]) + > $output +]]> + </command> + <inputs> + <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> + <param name="extract" type="text" label="Extract" size="160" help="Need help? See below a few examples." /> + <param name="one_effect_per_line" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="One effect per line" help="When variants have more than one effect, lists one effect per line, while all other parameters in the line are repeated across mutiple lines" /> + <param name="separator" type="text" value="" optional="true" label="multiple field separator" size="1" help="Separate multiple fields in one column with this character, e.g. a comma, rather than a column for each of the multiple values"> + </param> + <param name="empty_text" type="text" value="" optional="true" label="empty field text" size="10" help="Represent empty fields with this value, rather than leaving them blank" > + </param> + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + <tests> + <test> + <param name="input" ftype="vcf" value="test_rmInfo.vcf"/> + <param name="extract" value="CHROM POS REF ALT EFF[*].EFFECT"/> + <output name="output"> + <assert_contents> + <has_text text="INTRAGENIC" /> + <not_has_text text="DOWNSTREAM,INTRAGENIC,INTRON,UTR_3_PRIME" /> + </assert_contents> + </output> + </test> + + <test> + <param name="input" ftype="vcf" value="test_rmInfo.vcf"/> + <param name="extract" value="CHROM POS REF ALT EFF[*].EFFECT"/> + <param name="separator" value=","/> + <output name="output"> + <assert_contents> + <has_text text="DOWNSTREAM,INTRAGENIC,INTRON,UTR_3_PRIME" /> + </assert_contents> + </output> + </test> + + </tests> + <help><![CDATA[ + +**SnpSift Extract Fields** + +Extract fields from a VCF file to a TXT, tab separated format, that you can easily load in R, XLS, etc. + +http://snpeff.sourceforge.net/SnpSift.html#Extract + +You can also use sub-fields and genotype fields / sub-fields such as: + + :: + + Standard VCF fields: + CHROM + POS + ID + REF + ALT + FILTER + INFO fields: + AF + AC + DP + MQ + etc. (any info field available) + SnpEff 'ANN' fields: + "ANN[*].ALLELE" (alias GENOTYPE) + "ANN[*].EFFECT" (alias ANNOTATION): Effect in Sequence ontology terms (e.g. 'missense_variant', 'synonymous_variant', 'stop_gained', etc.) + "ANN[*].IMPACT:" { HIGH, MODERATE, LOW, MODIFIER } + "ANN[*].GENE:" Gene name (e.g. 'PSD3') + "ANN[*].GENEID:" Gene ID + "ANN[*].FEATURE + " ANN[*].FEATUREID (alias TRID: Transcript ID) + "ANN[*].BIOTYPE:" Biotype, as described by the annotations (e.g. 'protein_coding') + "ANN[*].RANK:" Exon or Intron rank (i.e. exon number in a transcript) + "ANN[*].HGVS_C" (alias HGVS_DNA, CODON): Variant in HGVS (DNA) notation + "ANN[*].HGVS_P" (alias HGVS, HGVS_PROT, AA): Variant in HGVS (protein) notation + "ANN[*].CDNA_POS" (alias POS_CDNA) + "ANN[*].CDNA_LEN" (alias LEN_CDNA) + "ANN[*].CDS_POS" (alias POS_CDS) + "ANN[*].CDS_LEN" (alias LEN_CDS) + "ANN[*].AA_POS" (alias POS_AA) + "ANN[*].AA_LEN" (alias LEN_AA) + "ANN[*].DISTANCE" + "ANN[*].ERRORS" (alias WARNING, INFOS) + SnpEff 'EFF' fields (this is for older SnpEff/SnpSift versions, new version use 'ANN' field): + "EFF[*].EFFECT" + "EFF[*].IMPACT" + "EFF[*].FUNCLASS" + "EFF[*].CODON" + "EFF[*].AA" + "EFF[*].AA_LEN" + "EFF[*].GENE" + "EFF[*].BIOTYPE" + "EFF[*].CODING" + "EFF[*].TRID" + "EFF[*].RANK" + SnpEff 'LOF' fields: + "LOF[*].GENE" + "LOF[*].GENEID" + "LOF[*].NUMTR" + "LOF[*].PERC" + SnpEff' NMD' fields: + "NMD[*].GENE" + "NMD[*].GENEID" + "NMD[*].NUMTR" + "NMD[*].PERC" + + +Some examples: + + - *Extracting chromosome, position, ID and allele frequency from a VCF file:* + + **CHROM POS ID AF** + + The result will look something like: + + :: + + #CHROM POS ID AF + 1 69134 0.086 + 1 69496 rs150690004 0.001 + + + - *Extracting genotype fields:* + + **CHROM POS ID THETA GEN[0].GL[1] GEN[1].GL GEN[3].GL[*] GEN[*].GT** + + This means to extract: + + - CHROM POS ID: regular fields (as in the previous example) + - THETA : This one is from INFO + - GEN[0].GL[1] : Second likelihood from first genotype + - GEN[1].GL : The whole GL fiels (all entries without separating them) + - GEN[3].GL[*] : All likelihoods form genotype 3 (this time they will be tab separated, as opposed to the previous one). + - GEN[*].GT : Genotype subfields (GT) from ALL samples (tab separated). + + The result will look something like: + + :: + + #CHROM POS ID THETA GEN[0].GL[1] GEN[1].GL GEN[3].GL[*] GEN[*].GT + 1 10583 rs58108140 0.0046 -0.47 -0.24,-0.44,-1.16 -0.48 -0.48 -0.48 0|0 0|0 0|0 0|1 0|0 0|1 0|0 0|0 0|1 + 1 10611 rs189107123 0.0077 -0.48 -0.24,-0.44,-1.16 -0.48 -0.48 -0.48 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 + 1 13302 rs180734498 0.0048 -0.58 -2.45,-0.00,-5.00 -0.48 -0.48 -0.48 0|0 0|1 0|0 0|0 0|0 1|0 0|0 0|1 0|0 + + - *Extracting fields with multiple values:* + (notice that there are multiple effect columns per line because there are mutiple effects per variant) + + **CHROM POS REF ALT ANN[*].EFFECT** + + The result will look something like: + + :: + + #CHROM POS REF ALT ANN[*].EFFECT + 22 17071756 T C 3_prime_UTR_variant downstream_gene_variant + 22 17072035 C T missense_variant downstream_gene_variant + 22 17072258 C A missense_variant downstream_gene_variant + + - *Extracting fields with multiple values using a comma as a multipe field separator:* + + **CHROM POS REF ALT ANN[*].EFFECT ANN[*].HGVS_P** + + The result will look something like: + + :: + + #CHROM POS REF ALT ANN[*].EFFECT ANN[*].HGVS_P + 22 17071756 T C 3_prime_UTR_variant,downstream_gene_variant .,. + 22 17072035 C T missense_variant,downstream_gene_variant p.Gly469Glu,. + 22 17072258 C A missense_variant,downstream_gene_variant p.Gly395Cys,. + + + - *Extracting fields with multiple values, one effect per line:* + + **CHROM POS REF ALT ANN[*].EFFECT** + + The result will look something like: + + :: + + #CHROM POS REF ALT ANN[*].EFFECT + 22 17071756 T C 3_prime_UTR_variant + 22 17071756 T C downstream_gene_variant + 22 17072035 C T missense_variant + 22 17072035 C T downstream_gene_variant + 22 17072258 C A missense_variant + 22 17072258 C A downstream_gene_variant + + +@EXTERNAL_DOCUMENTATION@ + http://snpeff.sourceforge.net/SnpSift.html#Extract + +@CITATION_SECTION@ + +]]> + </help> +</tool>