| Previous changeset 4:b04635ebfab0 (2017-10-24) Next changeset 6:2b3e65a4252f (2019-01-16) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b |
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modified:
snpSift_annotate.xml snpSift_caseControl.xml snpSift_extractFields.xml snpSift_filter.xml snpSift_int.xml snpSift_macros.xml snpSift_rmInfo.xml snpSift_vartype.xml snpSift_vcfCheck.xml |
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added:
test-data/extFields_test3_in.vcf test-data/extFields_test3_out.vcf |
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| diff -r b04635ebfab0 -r 09d6806c609e snpSift_annotate.xml --- a/snpSift_annotate.xml Tue Oct 24 07:28:17 2017 -0400 +++ b/snpSift_annotate.xml Wed Apr 18 07:28:51 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="snpSift_annotate" name="SnpSift Annotate" version="@WRAPPER_VERSION@.0"> +<tool id="snpSift_annotate" name="SnpSift Annotate" version="@WRAPPER_VERSION@.galaxy0"> <description>SNPs from dbSnp</description> <!-- You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) |
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| diff -r b04635ebfab0 -r 09d6806c609e snpSift_caseControl.xml --- a/snpSift_caseControl.xml Tue Oct 24 07:28:17 2017 -0400 +++ b/snpSift_caseControl.xml Wed Apr 18 07:28:51 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="snpSift_caseControl" name="SnpSift CaseControl" version="@WRAPPER_VERSION@.0"> +<tool id="snpSift_caseControl" name="SnpSift CaseControl" version="@WRAPPER_VERSION@.galaxy0"> <description>Count samples are in 'case' and 'control' groups.</description> <!-- You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) |
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| diff -r b04635ebfab0 -r 09d6806c609e snpSift_extractFields.xml --- a/snpSift_extractFields.xml Tue Oct 24 07:28:17 2017 -0400 +++ b/snpSift_extractFields.xml Wed Apr 18 07:28:51 2018 -0400 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="snpSift_extractFields" name="SnpSift Extract Fields" version="@WRAPPER_VERSION@.0">\n+<tool id="snpSift_extractFields" name="SnpSift Extract Fields" version="@WRAPPER_VERSION@.galaxy0">\n <options sanitize="False" />\n <description>from a VCF file into a tabular file</description>\n <macros>\n@@ -9,27 +9,27 @@\n <expand macro="version_command" />\n <command><![CDATA[\n @CONDA_SNPSIFT_JAR_PATH@ &&\n-cat \'$input\'\n+cat \'${input}\'\n #if $one_effect_per_line:\n- | "\\$SNPSIFT_JAR_PATH/scripts/vcfEffOnePerLine.pl"\n+ | perl "\\$SNPSIFT_JAR_PATH/scripts/vcfEffOnePerLine.pl"\n #end if\n | SnpSift -Xmx6G extractFields\n #if $separator:\n- -s \'$separator\'\n+ -s \'${separator}\'\n #end if\n #if $empty_text:\n- -e \'$empty_text\'\n+ -e \'${empty_text}\'\n #end if\n -\n #echo \' \'.join([\'"%s"\' % x for x in $extract.split()])\n-> \'$output\'\n+> \'${output}\'\n ]]></command>\n <inputs>\n <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>\n- <param name="extract" type="text" label="Extract" help="Need help? See below a few examples." />\n+ <param name="extract" type="text" label="Fields to extract" value="CHROM POS ID REF ALT FILTER" help="Separated by spaces. See help below for an explanation" />\n <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" />\n- <param name="separator" type="text" value="" label="multiple field separator" help="Separate multiple fields in one column with this character, e.g. a comma, rather than a column for each of the multiple values" />\n- <param name="empty_text" type="text" value="" label="empty field text" help="Represent empty fields with this value, rather than leaving them blank" />\n+ <param name="separator" type="text" value="" label="multiple field separator" help="Separate multiple fields in one column with this character, e.g. a comma, rather than a column for each of the multiple values" argument="-s" />\n+ <param name="empty_text" type="text" value="" label="empty field text" help="Represent empty fields with this value, rather than leaving them blank" argument="-e"/>\n </inputs>\n <outputs>\n <data name="output" format="tabular" />\n@@ -40,156 +40,171 @@\n <param name="extract" value="CHROM POS REF ALT EFF[*].EFFECT"/>\n <output name="output">\n <assert_contents>\n- <has_text text="INTRAGENIC" />\n- <not_has_text text="DOWNSTREAM,INTRAGENIC,INTRON,UTR_3_PRIME" />\n+ <has_text text="INTRAGENIC" />\n+ <not_has_text text="DOWNSTREAM,INTRAGENIC,INTRON,UTR_3_PRIME" />\n </assert_contents>\n </output>\n </test>\n-\n <test>\n <param name="input" ftype="vcf" value="test_rmInfo.vcf"/>\n <param name="extract" value="CHROM POS REF ALT EFF[*].EFFECT"/>\n <param name="separator" value=","/>\n <output name="output">\n <assert_contents>\n-\t\t<has_text text="DOWNSTREAM,INTRAGENIC,INTRON,UTR_3_PRIME" />\n+ <has_text text="DOWNSTREAM,INTRAGENIC,INTRON,UTR_3_PRIME" />\n </assert_contents>\n </output>\n </test>\n+ <test>\n+ <param name="input" ftype="vcf" value="extFields_test3_in.vcf"/>\n+ <param name="extract" value="CHROM POS ID REF ALT FILTER ANN[*].EFFECT"/>\n+ <param name="one_effect_per_line" value="true"/>\n+ <output name="output" value="extFields_test3_out.vcf"/>\n+ </test>\n </tests>\n <help><![CDATA[\n-**SnpSift Extract Fields**\n+**What is does**\n+\n+`SnpSift Extract Fields <http://snpeff.sourceforge.net/SnpSift.html#Extract>`_ selects columns from a VCF dataset'..b' 0|0 0|1\n- 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\n- 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\n+The result will look something like::\n \n-- *Extracting fields with multiple values*:\n- (notice that there are multiple effect columns per line because there are mutiple effects per variant)\n+ #CHROM POS ID THETA GEN[0].GL[1] GEN[1].GL GEN[3].GL[*] GEN[*].GT\n+ 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\n+ 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\n+ 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\n \n- **CHROM POS REF ALT ANN[*].EFFECT**\n+*Extracting fields with multiple values*:\n+ (notice that there are multiple effect columns per line because there are multiple effects per variant)\n \n- The result will look something like::\n+**CHROM POS REF ALT ANN[*].EFFECT**\n+\n+The result will look something like::\n \n- #CHROM\tPOS\tREF\tALT\tANN[*].EFFECT\n- 22\t17071756\tT\tC\t3_prime_UTR_variant\tdownstream_gene_variant\n- 22\t17072035\tC\tT\tmissense_variant\tdownstream_gene_variant\n- 22\t17072258\tC\tA\tmissense_variant\tdownstream_gene_variant\n+ #CHROM POS REF ALT ANN[*].EFFECT\n+ 22 17071756 T C 3_prime_UTR_variant downstream_gene_variant\n+ 22 17072035 C T missense_variant downstream_gene_variant\n+ 22 17072258 C A missense_variant downstream_gene_variant\n \n-- *Extracting fields with multiple values using a comma as a multipe field separator:*\n+*Extracting fields with multiple values using a comma as a multiple field separator:*\n \n- **CHROM POS REF ALT ANN[*].EFFECT ANN[*].HGVS_P**\n+**CHROM POS REF ALT ANN[*].EFFECT ANN[*].HGVS_P**\n \n- The result will look something like::\n+The result will look something like::\n \n- #CHROM\tPOS\tREF\tALT\tANN[*].EFFECT\tANN[*].HGVS_P\n- 22\t17071756\tT\tC\t3_prime_UTR_variant,downstream_gene_variant\t.,.\n- 22\t17072035\tC\tT\tmissense_variant,downstream_gene_variant\tp.Gly469Glu,.\n- 22\t17072258\tC\tA\tmissense_variant,downstream_gene_variant\tp.Gly395Cys,.\n+ #CHROM POS REF ALT ANN[*].EFFECT ANN[*].HGVS_P\n+ 22 17071756 T C 3_prime_UTR_variant,downstream_gene_variant .,.\n+ 22 17072035 C T missense_variant,downstream_gene_variant p.Gly469Glu,.\n+ 22 17072258 C A missense_variant,downstream_gene_variant p.Gly395Cys,.\n \n-- *Extracting fields with multiple values, one effect per line:*\n+*Extracting fields with multiple values, one effect per line:*\n \n- **CHROM POS REF ALT ANN[*].EFFECT**\n+**CHROM POS REF ALT ANN[*].EFFECT**\n \n- The result will look something like::\n+The result will look something like::\n \n- #CHROM\tPOS\tREF\tALT\tANN[*].EFFECT\n- 22\t17071756\tT\tC\t3_prime_UTR_variant\n- 22\t17071756\tT\tC\tdownstream_gene_variant\n- 22\t17072035\tC\tT\tmissense_variant\n- 22\t17072035\tC\tT\tdownstream_gene_variant\n- 22\t17072258\tC\tA\tmissense_variant\n- 22\t17072258\tC\tA\tdownstream_gene_variant\n+ #CHROM POS REF ALT ANN[*].EFFECT\n+ 22 17071756 T C 3_prime_UTR_variant\n+ 22 17071756 T C downstream_gene_variant\n+ 22 17072035 C T missense_variant\n+ 22 17072035 C T downstream_gene_variant\n+ 22 17072258 C A missense_variant\n+ 22 17072258 C A downstream_gene_variant\n \n @EXTERNAL_DOCUMENTATION@\n - http://snpeff.sourceforge.net/SnpSift.html#Extract\n' |
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| diff -r b04635ebfab0 -r 09d6806c609e snpSift_filter.xml --- a/snpSift_filter.xml Tue Oct 24 07:28:17 2017 -0400 +++ b/snpSift_filter.xml Wed Apr 18 07:28:51 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="snpSift_filter" name="SnpSift Filter" version="@WRAPPER_VERSION@.0"> +<tool id="snpSift_filter" name="SnpSift Filter" version="@WRAPPER_VERSION@.galaxy0"> <description>Filter variants using arbitrary expressions</description> <macros> <import>snpSift_macros.xml</import> |
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| diff -r b04635ebfab0 -r 09d6806c609e snpSift_int.xml --- a/snpSift_int.xml Tue Oct 24 07:28:17 2017 -0400 +++ b/snpSift_int.xml Wed Apr 18 07:28:51 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="snpSift_int" name="SnpSift Intervals" version="@WRAPPER_VERSION@.0"> +<tool id="snpSift_int" name="SnpSift Intervals" version="@WRAPPER_VERSION@.galaxy0"> <description>Filter variants using intervals</description> <!-- You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) |
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| diff -r b04635ebfab0 -r 09d6806c609e snpSift_macros.xml --- a/snpSift_macros.xml Tue Oct 24 07:28:17 2017 -0400 +++ b/snpSift_macros.xml Wed Apr 18 07:28:51 2018 -0400 |
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| @@ -1,7 +1,11 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="4.3.1p">snpsift</requirement> + <requirement type="package" version="4.3.1t">snpsift</requirement> + <!--Coreutils are required to make readlink work across platforms. Previous version did not work on MacOS--> + <requirement type="package" version="8.25">coreutils</requirement> + <!--PERL is required to make SnpSift helper scripts run--> + <requirement type="package" version="5.26">perl</requirement> </requirements> </xml> <xml name="stdio"> @@ -16,7 +20,7 @@ SnpSift dbnsfp 2>&1|head -n 1 ]]></version_command> </xml> - <token name="@WRAPPER_VERSION@">4.3</token> + <token name="@WRAPPER_VERSION@">4.3+t</token> <token name="@EXTERNAL_DOCUMENTATION@"> For details about this tool, please go to: |
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| diff -r b04635ebfab0 -r 09d6806c609e snpSift_rmInfo.xml --- a/snpSift_rmInfo.xml Tue Oct 24 07:28:17 2017 -0400 +++ b/snpSift_rmInfo.xml Wed Apr 18 07:28:51 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="snpSift_rmInfo" name="SnpSift rmInfo" version="@WRAPPER_VERSION@.0"> +<tool id="snpSift_rmInfo" name="SnpSift rmInfo" version="@WRAPPER_VERSION@.galaxy0"> <description>remove INFO field annotations</description> <macros> <import>snpSift_macros.xml</import> |
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| diff -r b04635ebfab0 -r 09d6806c609e snpSift_vartype.xml --- a/snpSift_vartype.xml Tue Oct 24 07:28:17 2017 -0400 +++ b/snpSift_vartype.xml Wed Apr 18 07:28:51 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="snpsift_vartype" name="SnpSift Variant Type" version="@WRAPPER_VERSION@.1"> +<tool id="snpsift_vartype" name="SnpSift Variant Type" version="@WRAPPER_VERSION@.galaxy0"> <description>Annotate with variant type</description> <macros> <import>snpSift_macros.xml</import> |
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| diff -r b04635ebfab0 -r 09d6806c609e snpSift_vcfCheck.xml --- a/snpSift_vcfCheck.xml Tue Oct 24 07:28:17 2017 -0400 +++ b/snpSift_vcfCheck.xml Wed Apr 18 07:28:51 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="@WRAPPER_VERSION@.0"> +<tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="@WRAPPER_VERSION@.galaxy0"> <description>basic checks for VCF specification compliance</description> <macros> <import>snpSift_macros.xml</import> |
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| diff -r b04635ebfab0 -r 09d6806c609e test-data/extFields_test3_in.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/extFields_test3_in.vcf Wed Apr 18 07:28:51 2018 -0400 |
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| b'@@ -0,0 +1,78 @@\n+##fileformat=VCFv4.2\n+##fileDate=20180328\n+##source=freeBayes v1.1.0-46-g8d2b3a0-dirty\n+##reference=localref.fa\n+##contig=<ID=U00096,length=4639675>\n+##phasing=none\n+##commandline="freebayes --region U00096:0..4639675 --bam b_0.bam --bam b_1.bam --bam b_2.bam --bam b_3.bam --bam b_4.bam --bam b_5.bam --bam b_6.bam --bam b_7.bam --bam b_8.bam --bam b_9.bam --bam b_10.bam --bam b_11.bam --bam b_12.bam --fasta-reference localref.fa --vcf ./vcf_output/part_U00096:0..4639675.vcf --theta 0.001 --ploidy 1 -K -m 20 -q 20 -R 0 -Y 0 -e 1000 -F 0.2 -C 2 -G 1 --min-coverage 0 --min-alternate-qsum 0"\n+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">\n+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">\n+##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">\n+##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">\n+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">\n+##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">\n+##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">\n+##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">\n+##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">\n+##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">\n+##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">\n+##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">\n+##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations">\n+##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations">\n+##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">\n+##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">\n+##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand">\n+##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand">\n+##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding\'s inequality">\n+##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding\'s inequality">\n+##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">\n+##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding\'s inequality">\n+##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">\n+##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding\'s inequality">\n+##INFO=<ID=RPPR,Number=1,Type=Floa'..b'riant(MODIFIER||1282|c.-1282A>C|350|yncI|protein_coding|CODING|b1459||C|WARNING_TRANSCRIPT_NO_START_CODON),upstream_gene_variant(MODIFIER||2512|c.-2512A>C|378|ydcC|protein_coding|CODING|b1460||C),upstream_gene_variant(MODIFIER||3748|c.-3748A>C|77|pptA|protein_coding|CODING|b1461||C),upstream_gene_variant(MODIFIER||4720|c.-4720A>C|281|nhoA|protein_coding|CODING|b1463||C),downstream_gene_variant(MODIFIER||4936|c.*4936A>C|353|yncE|protein_coding|CODING|b1452||C),downstream_gene_variant(MODIFIER||2440|c.*2440A>C|205|yncG|protein_coding|CODING|b1454||C),downstream_gene_variant(MODIFIER||2152|c.*2152A>C|70|yncH|protein_coding|CODING|b1455||C),downstream_gene_variant(MODIFIER||3978|c.*3978T>G|189|yddH|protein_coding|CODING|b1462||C)\tGT:DP:AD:RO:QR:AO:QA:GL\t0:22:17,5:17:627:5:112:0,-46.4475\t0:11:10,1:10:378:1:22:0,-32.1693\t0:33:31,2:31:1151:2:49:0,-99.2161\n+U00096\t1532370\t.\tG\tT\t7.50367E-15\t.\tAB=0;ABP=0;AC=0;AF=0;AN=12;AO=2;CIGAR=1X;DP=378;DPB=378;DPRA=0.268293;EPP=3.0103;EPPR=19.9408;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=12;NUMALT=1;ODDS=74.0204;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=13838;RO=374;RPL=2;RPP=7.35324;RPPR=5.82044;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=216;SRP=22.5419;SRR=158;TYPE=snp;technology.ILLUMINA=1;EFF=missense_variant(MODERATE|MISSENSE|cGt/cTt|p.Arg108Leu/c.323G>T|281|nhoA|protein_coding|CODING|b1463|1|T),upstream_gene_variant(MODIFIER||495|c.-495C>A|189|yddH|protein_coding|CODING|b1462||T),downstream_gene_variant(MODIFIER||4408|c.*4408G>T|678|rhsE|protein_coding|CODING|b1456||T|WARNING_TRANSCRIPT_NO_START_CODON),downstream_gene_variant(MODIFIER||3942|c.*3942G>T|160|ydcD|protein_coding|CODING|b1457||T),downstream_gene_variant(MODIFIER||2707|c.*2707G>T|350|yncI|protein_coding|CODING|b1459||T|WARNING_TRANSCRIPT_NO_START_CODON),downstream_gene_variant(MODIFIER||1394|c.*1394G>T|378|ydcC|protein_coding|CODING|b1460||T),downstream_gene_variant(MODIFIER||1061|c.*1061G>T|77|pptA|protein_coding|CODING|b1461||T),downstream_gene_variant(MODIFIER||619|c.*619C>A|297|yddE|protein_coding|CODING|b1464||T),downstream_gene_variant(MODIFIER||1591|c.*1591C>A|226|narV|protein_coding|CODING|b1465||T),downstream_gene_variant(MODIFIER||2268|c.*2268C>A|231|narW|protein_coding|CODING|b1466||T),downstream_gene_variant(MODIFIER||2963|c.*2963C>A|514|narY|protein_coding|CODING|b1467||T),downstream_gene_variant(MODIFIER||4504|c.*4504C>A|1246|narZ|protein_coding|CODING|b1468||T)\tGT:DP:AD:RO:QR:AO:QA:GL\t0:16:16,0:16:583:0:0:0,-52.8004\t0:9:7,2:7:249:2:76:0,-15.539\t0:46:46,0:46:1675:0:0:0,-151.009\n+U00096\t1533613\t.\tT\tC\t6.56972E-15\t.\tAB=0;ABP=0;AC=0;AF=0;AN=13;AO=2;CIGAR=1X;DP=489;DPB=489;DPRA=0.0989691;EPP=3.0103;EPPR=70.4686;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.9979;NS=13;NUMALT=1;ODDS=41.1942;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=80;QR=18551;RO=487;RPL=0;RPP=7.35324;RPPR=96.7582;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=203;SRP=32.265;SRR=284;TYPE=snp;technology.ILLUMINA=1;EFF=synonymous_variant(LOW|SILENT|ggA/ggG|p.Gly90Gly/c.270A>G|297|yddE|protein_coding|CODING|b1464|1|C),upstream_gene_variant(MODIFIER||1738|c.-1738A>G|189|yddH|protein_coding|CODING|b1462||C),downstream_gene_variant(MODIFIER||3950|c.*3950T>C|350|yncI|protein_coding|CODING|b1459||C|WARNING_TRANSCRIPT_NO_START_CODON),downstream_gene_variant(MODIFIER||2637|c.*2637T>C|378|ydcC|protein_coding|CODING|b1460||C),downstream_gene_variant(MODIFIER||2304|c.*2304T>C|77|pptA|protein_coding|CODING|b1461||C),downstream_gene_variant(MODIFIER||720|c.*720T>C|281|nhoA|protein_coding|CODING|b1463||C),downstream_gene_variant(MODIFIER||348|c.*348A>G|226|narV|protein_coding|CODING|b1465||C),downstream_gene_variant(MODIFIER||1025|c.*1025A>G|231|narW|protein_coding|CODING|b1466||C),downstream_gene_variant(MODIFIER||1720|c.*1720A>G|514|narY|protein_coding|CODING|b1467||C),downstream_gene_variant(MODIFIER||3261|c.*3261A>G|1246|narZ|protein_coding|CODING|b1468||C)\tGT:DP:AD:RO:QR:AO:QA:GL\t0:26:26,0:26:1013:0:0:0,-91.465\t0:11:11,0:11:417:0:0:0,-37.8758\t0:58:58,0:58:2210:0:0:0,-199.104\n' |
| b |
| diff -r b04635ebfab0 -r 09d6806c609e test-data/extFields_test3_out.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/extFields_test3_out.vcf Wed Apr 18 07:28:51 2018 -0400 |
| [ |
| @@ -0,0 +1,129 @@ +CHROM POS ID REF ALT FILTER ANN[*].EFFECT +U00096 1518079 T G synonymous_variant +U00096 1518079 T G upstream_gene_variant +U00096 1518079 T G upstream_gene_variant +U00096 1518079 T G upstream_gene_variant +U00096 1518079 T G upstream_gene_variant +U00096 1518079 T G upstream_gene_variant +U00096 1518079 T G downstream_gene_variant +U00096 1518079 T G downstream_gene_variant +U00096 1518079 T G downstream_gene_variant +U00096 1518079 T G downstream_gene_variant +U00096 1518079 T G downstream_gene_variant +U00096 1518079 T G downstream_gene_variant +U00096 1518212 T A upstream_gene_variant +U00096 1518212 T A upstream_gene_variant +U00096 1518212 T A upstream_gene_variant +U00096 1518212 T A upstream_gene_variant +U00096 1518212 T A upstream_gene_variant +U00096 1518212 T A downstream_gene_variant +U00096 1518212 T A downstream_gene_variant +U00096 1518212 T A downstream_gene_variant +U00096 1518212 T A downstream_gene_variant +U00096 1518212 T A downstream_gene_variant +U00096 1518212 T A downstream_gene_variant +U00096 1518212 T A downstream_gene_variant +U00096 1518212 T A intergenic_region +U00096 1523784 G A missense_variant +U00096 1523784 G A upstream_gene_variant +U00096 1523784 G A upstream_gene_variant +U00096 1523784 G A upstream_gene_variant +U00096 1523784 G A upstream_gene_variant +U00096 1523784 G A upstream_gene_variant +U00096 1523784 G A upstream_gene_variant +U00096 1523784 G A downstream_gene_variant +U00096 1523784 G A downstream_gene_variant +U00096 1524994 CTTT CT frameshift_variant +U00096 1524994 CTTT CT upstream_gene_variant +U00096 1524994 CTTT CT upstream_gene_variant +U00096 1524994 CTTT CT upstream_gene_variant +U00096 1524994 CTTT CT upstream_gene_variant +U00096 1524994 CTTT CT upstream_gene_variant +U00096 1524994 CTTT CT upstream_gene_variant +U00096 1524994 CTTT CT downstream_gene_variant +U00096 1524994 CTTT CT downstream_gene_variant +U00096 1525214 T A upstream_gene_variant +U00096 1525214 T A upstream_gene_variant +U00096 1525214 T A upstream_gene_variant +U00096 1525214 T A upstream_gene_variant +U00096 1525214 T A upstream_gene_variant +U00096 1525214 T A upstream_gene_variant +U00096 1525214 T A downstream_gene_variant +U00096 1525214 T A downstream_gene_variant +U00096 1525214 T A downstream_gene_variant +U00096 1525214 T A intergenic_region +U00096 1525377 AGG AGGG,AGT upstream_gene_variant +U00096 1525377 AGG AGGG,AGT upstream_gene_variant +U00096 1525377 AGG AGGG,AGT upstream_gene_variant +U00096 1525377 AGG AGGG,AGT upstream_gene_variant +U00096 1525377 AGG AGGG,AGT upstream_gene_variant +U00096 1525377 AGG AGGG,AGT upstream_gene_variant +U00096 1525377 AGG AGGG,AGT upstream_gene_variant +U00096 1525377 AGG AGGG,AGT upstream_gene_variant +U00096 1525377 AGG AGGG,AGT upstream_gene_variant +U00096 1525377 AGG AGGG,AGT upstream_gene_variant +U00096 1525377 AGG AGGG,AGT upstream_gene_variant +U00096 1525377 AGG AGGG,AGT upstream_gene_variant +U00096 1525377 AGG AGGG,AGT downstream_gene_variant +U00096 1525377 AGG AGGG,AGT downstream_gene_variant +U00096 1525377 AGG AGGG,AGT downstream_gene_variant +U00096 1525377 AGG AGGG,AGT downstream_gene_variant +U00096 1525377 AGG AGGG,AGT downstream_gene_variant +U00096 1525377 AGG AGGG,AGT downstream_gene_variant +U00096 1525377 AGG AGGG,AGT intergenic_region +U00096 1525377 AGG AGGG,AGT intergenic_region +U00096 1527079 A G missense_variant +U00096 1527079 A G upstream_gene_variant +U00096 1527079 A G upstream_gene_variant +U00096 1527079 A G upstream_gene_variant +U00096 1527079 A G upstream_gene_variant +U00096 1527079 A G upstream_gene_variant +U00096 1527079 A G upstream_gene_variant +U00096 1527079 A G downstream_gene_variant +U00096 1527079 A G downstream_gene_variant +U00096 1527079 A G downstream_gene_variant +U00096 1527079 A G downstream_gene_variant +U00096 1527291 G T missense_variant +U00096 1527291 G T upstream_gene_variant +U00096 1527291 G T upstream_gene_variant +U00096 1527291 G T upstream_gene_variant +U00096 1527291 G T upstream_gene_variant +U00096 1527291 G T upstream_gene_variant +U00096 1527291 G T upstream_gene_variant +U00096 1527291 G T downstream_gene_variant +U00096 1527291 G T downstream_gene_variant +U00096 1527291 G T downstream_gene_variant +U00096 1527291 G T downstream_gene_variant +U00096 1527328 A C missense_variant +U00096 1527328 A C upstream_gene_variant +U00096 1527328 A C upstream_gene_variant +U00096 1527328 A C upstream_gene_variant +U00096 1527328 A C upstream_gene_variant +U00096 1527328 A C upstream_gene_variant +U00096 1527328 A C upstream_gene_variant +U00096 1527328 A C downstream_gene_variant +U00096 1527328 A C downstream_gene_variant +U00096 1527328 A C downstream_gene_variant +U00096 1527328 A C downstream_gene_variant +U00096 1532370 G T missense_variant +U00096 1532370 G T upstream_gene_variant +U00096 1532370 G T downstream_gene_variant +U00096 1532370 G T downstream_gene_variant +U00096 1532370 G T downstream_gene_variant +U00096 1532370 G T downstream_gene_variant +U00096 1532370 G T downstream_gene_variant +U00096 1532370 G T downstream_gene_variant +U00096 1532370 G T downstream_gene_variant +U00096 1532370 G T downstream_gene_variant +U00096 1532370 G T downstream_gene_variant +U00096 1532370 G T downstream_gene_variant +U00096 1533613 T C synonymous_variant +U00096 1533613 T C upstream_gene_variant +U00096 1533613 T C downstream_gene_variant +U00096 1533613 T C downstream_gene_variant +U00096 1533613 T C downstream_gene_variant +U00096 1533613 T C downstream_gene_variant +U00096 1533613 T C downstream_gene_variant +U00096 1533613 T C downstream_gene_variant +U00096 1533613 T C downstream_gene_variant +U00096 1533613 T C downstream_gene_variant |