| Next changeset 1:0bc800d67a0e (2018-07-15) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 |
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added:
macros.xml test-data/N_Region_Chr1_CDKN2C.pileup.gz test-data/T_Region_Chr1_CDKN2C.pileup.gz test-data/test_in1.pileup test-data/varscan_copynumber_result1.interval test-data/varscan_mpileup_result1.vcf test-data/varscan_somatic_indel_result1.vcf test-data/varscan_somatic_snp_result1.vcf varscan_mpileup.xml |
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| diff -r 000000000000 -r 1e667badbe87 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Jul 10 13:36:03 2018 -0400 |
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| @@ -0,0 +1,57 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">varscan</requirement> + <requirement type="package" version="4.2.1">gawk</requirement> + <yield/> + </requirements> + </xml> + + <token name="@VERSION@">2.4.3</token> + + <xml name="stdio"> + <stdio> + <regex match="Exception" source="both" level="fatal" description="Tool exception"/> + <regex match=".*" source="both" level="log" description="tool progress"/> + </stdio> + <version_command><![CDATA[varscan 2>&1 | head -n 1]]></version_command> + </xml> + + <xml name="citations"> + <citations> + <citation type="doi">10.1101/gr.129684.111</citation> + </citations> + </xml> + + <xml name="min_coverage"> + <param argument="--min-coverage" name="min_coverage" type="integer" value="8" min="1" max="200" + label="Minimum read depth" help="Minimum depth at a position to make a call"/> + </xml> + <xml name="min_reads2"> + <param argument="--min-reads2" name="min_reads2" type="integer" value="2" min="1" max="200" + label="Minimum supporting reads" help="Minimum supporting reads at a position to make a call"/> + </xml> + <xml name="min_avg_qual"> + <param argument="--min-avg-qual" name="min_avg_qual" type="integer" value="15" min="1" max="50" + label="Minimum base quality at a position to count a read"/> + </xml> + <xml name="min_var_freq" token_value="0.01"> + <param argument="--min-var-freq" name="min_var_freq" type="float" value="@VALUE@" min="0" max="1" + label="Minimum variant allele frequency threshold"/> + </xml> + <xml name="min_freq_for_hom"> + <param argument="--min-freq-for-hom" name="min_freq_for_hom" type="float" value="0.75" min="0" max="1" + label="Minimum frequency to call homozygote"/> + </xml> + <xml name="p_value" token_label="p-value threshold for calling variants" token_value="0.01"> + <param argument="--p-value" name="p_value" type="float" value="@VALUE@" min="0.0" max="1.0" + label="@LABEL@"/> + </xml> + <xml name="strand_filter"> + <param name="strand_filter" type="select" label="Ignore variants with >90% support on one strand"> + <option value="no" selected="True">no</option> + <option value="yes">yes</option> + </param> + </xml> + +</macros> |
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| diff -r 000000000000 -r 1e667badbe87 test-data/N_Region_Chr1_CDKN2C.pileup.gz |
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| Binary file test-data/N_Region_Chr1_CDKN2C.pileup.gz has changed |
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| diff -r 000000000000 -r 1e667badbe87 test-data/T_Region_Chr1_CDKN2C.pileup.gz |
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| Binary file test-data/T_Region_Chr1_CDKN2C.pileup.gz has changed |
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| diff -r 000000000000 -r 1e667badbe87 test-data/test_in1.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_in1.pileup Tue Jul 10 13:36:03 2018 -0400 |
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| @@ -0,0 +1,13 @@ +chr1 10087 a 41 ..+1C...........,,,,,.....C..C,...,..,,..c,.+1C A9D<<#C#<(C9ACAFF<?D>=(#;D#;AF=7898.GJ'6I +chr1 10088 c 41 .......T.....,,,,,.........,..A,..,,..,,. 2BBB<#B#A5?5?GJ;JD?@A?;#6B#HEG)GBBIB>IEE! +chr1 10089 c 41 .............,,,,,.........,...,..,,..,,. 8BBB<#D#?5A9AHJ;IFBBB??#6A#FEG8C=>H?FJ@C$ +chr1 10090 c 41 .............,,,,,.........,...,..,,..,,. 2#AB(#9#9(A<<GJEHEBBDA?#;;#D?H@5=CF1HJ;D' +chr1 10091 t 41 .............,,,,,A........,...,..,,..,,. (#(?5#,#<(?<?FIAF;(D=B9#;@#?#G8-=F=<CJ6BI +chr1 10092 a 41 .............,,,,,.........,...,..,,..,,. 9#9C<#5#9,5(<FH:GE9C?<?#3A#:#A@B8CC5EI=?J +chr1 10093 a 41 .............,,,,,.........,...c..,c..,,. ?#<DC#9#99?39CFEFC?D<(C#,C#1#HE'7G8'>I);J +chr1 10094 c 41 .............,,,,,.....G...,...,..,,..,,T ?#?B?#?#<8A8ABJBIG9D?9<#,?#F#IHH(AIGEHGH6 +chr1 10095 c 41 A............,,,,,.........,...,..,,..,,. ##8B<#A#??B8<EJCJB7BAAA#5B#>#>=F(@HHCIBH6 +chr1 10096 c 41 .............,,,,,........A,...,..,,..,,. ##ADA#B#18B?AHI<IE<AA?D#<;#C#E6B=FGCCIBE9 +chr1 10097 t 41 .............,,,,,.........,..C,..,,..-1A,,-1a. ##(B8#B#8(BB?AFAH:(B2??#<?#8#E'6;;B6@J8@J +chr1 10098 a 41 .............,,,,,.........,...,..,,.*,*. ##3C9#3#9999AFH2H;9D<C?#C3#?#E5?DAD@D!=$J +chr1 10099 a 41 .............,,,,,.........,...c..,,..,,. ##<D<#9#<9?<9FD+DF9CAA?#39#1#H?)C>9.D!.$J |
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| diff -r 000000000000 -r 1e667badbe87 test-data/varscan_copynumber_result1.interval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/varscan_copynumber_result1.interval Tue Jul 10 13:36:03 2018 -0400 |
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| @@ -0,0 +1,9 @@ +chrom chr_start chr_stop num_positions normal_depth tumor_depth log2_ratio gc_content +chr1 51436045 51436144 100 26.9 25.9 -0.052 51.0 +chr1 51436145 51436214 70 27.6 30.3 0.134 45.7 +chr1 51439427 51439526 100 31.1 29.3 -0.086 36.0 +chr1 51439527 51439626 100 85.3 86.0 0.012 44.0 +chr1 51439627 51439726 100 107.2 108.0 0.011 46.0 +chr1 51439727 51439826 100 70.8 80.3 0.183 58.0 +chr1 51439827 51439926 100 46.3 53.3 0.202 60.0 +chr1 51439927 51439960 34 27.5 35.9 0.383 52.9 |
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| diff -r 000000000000 -r 1e667badbe87 test-data/varscan_mpileup_result1.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/varscan_mpileup_result1.vcf Tue Jul 10 13:36:03 2018 -0400 |
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| @@ -0,0 +1,26 @@ +##fileformat=VCFv4.1 +##source=VarScan2 +##INFO=<ID=ADP,Number=1,Type=Integer,Description="Average per-sample depth of bases with Phred score >= 15"> +##INFO=<ID=WT,Number=1,Type=Integer,Description="Number of samples called reference (wild-type)"> +##INFO=<ID=HET,Number=1,Type=Integer,Description="Number of samples called heterozygous-variant"> +##INFO=<ID=HOM,Number=1,Type=Integer,Description="Number of samples called homozygous-variant"> +##INFO=<ID=NC,Number=1,Type=Integer,Description="Number of samples not called"> +##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand"> +##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Raw Read Depth as reported by SAMtools"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Quality Read Depth of bases with Phred score >= 15"> +##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)"> +##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)"> +##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency"> +##FORMAT=<ID=PVAL,Number=1,Type=String,Description="P-value from Fisher's Exact Test"> +##FORMAT=<ID=RBQ,Number=1,Type=Integer,Description="Average quality of reference-supporting bases (qual1)"> +##FORMAT=<ID=ABQ,Number=1,Type=Integer,Description="Average quality of variant-supporting bases (qual2)"> +##FORMAT=<ID=RDF,Number=1,Type=Integer,Description="Depth of reference-supporting bases on forward strand (reads1plus)"> +##FORMAT=<ID=RDR,Number=1,Type=Integer,Description="Depth of reference-supporting bases on reverse strand (reads1minus)"> +##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)"> +##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1 +chr1 10087 . A AC . PASS ADP=33;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:41:33:31:2:6.06%:9.8E-1:30:32:22:9:2:0 +chr1 10097 . TA T . PASS ADP=30;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:41:30:28:2:6.67%:9.8E-1:29:36:18:10:1:1 |
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| diff -r 000000000000 -r 1e667badbe87 test-data/varscan_somatic_indel_result1.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/varscan_somatic_indel_result1.vcf Tue Jul 10 13:36:03 2018 -0400 |
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| @@ -0,0 +1,18 @@ +##fileformat=VCFv4.1 +##source=VarScan2 +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total depth of quality bases"> +##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates if record is a somatic mutation"> +##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)"> +##INFO=<ID=SSC,Number=1,Type=String,Description="Somatic score in Phred scale (0-255) derived from somatic p-value"> +##INFO=<ID=GPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls"> +##INFO=<ID=SPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls"> +##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand"> +##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)"> +##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)"> +##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency"> +##FORMAT=<ID=DP4,Number=1,Type=String,Description="Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR |
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| diff -r 000000000000 -r 1e667badbe87 test-data/varscan_somatic_snp_result1.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/varscan_somatic_snp_result1.vcf Tue Jul 10 13:36:03 2018 -0400 |
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| @@ -0,0 +1,41 @@ +##fileformat=VCFv4.1 +##source=VarScan2 +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total depth of quality bases"> +##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates if record is a somatic mutation"> +##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)"> +##INFO=<ID=SSC,Number=1,Type=String,Description="Somatic score in Phred scale (0-255) derived from somatic p-value"> +##INFO=<ID=GPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls"> +##INFO=<ID=SPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls"> +##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand"> +##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)"> +##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)"> +##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency"> +##FORMAT=<ID=DP4,Number=1,Type=String,Description="Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR +chr1 51436072 . C A . PASS DP=47;SOMATIC;SS=2;SSC=3;GPV=1E0;SPV=4.4681E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:26:26:0:0%:23,3,0,0 0/1:.:21:20:1:4.76%:19,1,1,0 +chr1 51436311 . T C . PASS DP=16;SOMATIC;SS=2;SSC=3;GPV=1E0;SPV=4.375E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:9:9:0:0%:1,8,0,0 0/1:.:7:6:1:14.29%:0,6,0,1 +chr1 51436320 . G A . PASS DP=19;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.2632E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:9:9:0:0%:1,8,0,0 0/1:.:10:9:1:10%:0,9,0,1 +chr1 51439628 . T C . str10 DP=237;SOMATIC;SS=2;SSC=3;GPV=1E0;SPV=4.8101E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:123:123:0:0%:77,46,0,0 0/1:.:114:113:1:0.88%:74,39,0,1 +chr1 51439638 . G A . str10 DP=234;SOMATIC;SS=2;SSC=3;GPV=1E0;SPV=4.9145E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:119:119:0:0%:72,47,0,0 0/1:.:115:114:1:0.87%:75,39,0,1 +chr1 51439665 . C T . PASS DP=226;SOMATIC;SS=2;SSC=9;GPV=1E0;SPV=1.2006E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:114:114:0:0%:56,58,0,0 0/1:.:112:109:3:2.68%:63,46,2,1 +chr1 51439671 . G A . str10 DP=222;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.045E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:110:110:0:0%:53,57,0,0 0/1:.:112:111:1:0.89%:59,52,1,0 +chr1 51439684 . G T . str10 DP=210;SOMATIC;SS=2;SSC=3;GPV=1E0;SPV=4.9524E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:106:106:0:0%:51,55,0,0 0/1:.:104:103:1:0.96%:53,50,1,0 +chr1 51439703 . C T . str10 DP=202;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.099E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:99:99:0:0%:46,53,0,0 0/1:.:103:102:1:0.97%:48,54,0,1 +chr1 51439705 . G T . str10 DP=204;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.1961E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:98:98:0:0%:42,56,0,0 0/1:.:106:105:1:0.94%:48,57,0,1 +chr1 51439706 . G T . str10 DP=201;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.1741E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:97:97:0:0%:41,56,0,0 0/1:.:104:103:1:0.96%:46,57,1,0 +chr1 51439726 . C G . str10 DP=187;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.1872E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:90:90:0:0%:37,53,0,0 0/1:.:97:96:1:1.03%:44,52,1,0 +chr1 51439751 . C G . str10 DP=168;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.3293E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:79:78:0:0%:28,50,0,0 0/1:.:89:88:1:1.12%:35,53,0,1 +chr1 51439763 . G A . PASS DP=159;SOMATIC;SS=2;SSC=5;GPV=1E0;SPV=2.7092E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:76:76:0:0%:34,42,0,0 0/1:.:83:81:2:2.41%:32,49,1,1 +chr1 51439766 . G T . str10 DP=154;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.1299E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:75:75:0:0%:34,41,0,0 0/1:.:79:78:1:1.27%:30,48,0,1 +chr1 51439788 . T C . str10 DP=136;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.1471E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:66:66:0:0%:21,45,0,0 0/1:.:70:69:1:1.43%:24,45,1,0 +chr1 51439828 . G A . str10 DP=122;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.7377E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:52:52:0:0%:14,38,0,0 0/1:.:70:69:1:1.43%:27,42,0,1 +chr1 51439832 . C G . str10 DP=125;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.52E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:56:56:0:0%:14,42,0,0 0/1:.:69:68:1:1.45%:25,43,0,1 +chr1 51439876 . T G . str10 DP=105;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.619E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:46:46:0:0%:10,36,0,0 0/1:.:59:58:1:1.69%:23,35,0,1 +chr1 51439882 . G T . str10 DP=105;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.2381E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:50:50:0:0%:13,37,0,0 0/1:.:55:54:1:1.82%:22,32,0,1 +chr1 51439889 . G T . str10 DP=97;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.1546E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:47:47:0:0%:14,33,0,0 0/1:.:50:49:1:2%:21,28,0,1 +chr1 51439953 . G T . str10 DP=59;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.9322E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:24:24:0:0%:5,19,0,0 0/1:.:35:34:1:2.86%:7,27,0,1 +chr1 51440035 . G T . PASS DP=21;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=6.1905E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:8:8:0:0%:1,7,0,0 0/1:.:13:12:1:7.69%:1,11,0,1 |
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| diff -r 000000000000 -r 1e667badbe87 varscan_mpileup.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/varscan_mpileup.xml Tue Jul 10 13:36:03 2018 -0400 |
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| @@ -0,0 +1,101 @@ +<tool id="varscan_mpileup" name="VarScan mpileup" version="@VERSION@.0"> + <description>for variant detection</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <command><![CDATA[ + ## Set up samples list file. + #if $sample_names.strip() != '': + echo $sample_names | awk -F ',' '{ for (i = 1; i <= NF; i++) { print \$i; } }' > samples_list.txt && + #end if + + ## Set up command + input. + varscan ${cmd} '${input}' + --min-coverage ${min_coverage} + --min-reads2 ${min_reads2} + --min-avg-qual ${min_avg_qual} + --min-var-freq ${min_var_freq} + --min-freq-for-hom ${min_freq_for_hom} + --p-value ${p_value} + + #if str($strand_filter) == 'yes': + --strand-filter 1 + #end if + + ## Report only variants in consensus. + #if str($cmd) == 'mpileup2cns': + --variants + #end if + + ## Set up outputs. + --output-vcf 1 > '$output' + + #if $sample_names.strip() != '': + --vcf-sample-list samples_list.txt + #end if + + ]]></command> + <inputs> + <param name="input" format="pileup" type="data" label="Samtools pileup dataset" help=""/> + + <param name="cmd" type="select" label="Analysis type"> + <option value="mpileup2snp" selected="True">single nucleotide variation</option> + <option value="mpileup2indel">insertions and deletions</option> + <option value="mpileup2cns">consensus genotype</option> + </param> + + <expand macro="min_coverage" /> + <expand macro="min_reads2" /> + <expand macro="min_avg_qual" /> + <expand macro="min_var_freq" value="0.01" /> + <expand macro="min_freq_for_hom" /> + <expand macro="p_value" value="0.99" label="Default p-value threshold for calling variants"/> + <expand macro="strand_filter" /> + <param name="sample_names" type="text" value="" help="Separate sample names by comma; leave blank to use default sample names."/> + </inputs> + <outputs> + <data name="output" format="vcf"/> + </outputs> + <tests> + <test> + <param name="input" value="test_in1.pileup" /> + <param name="cmd" value="mpileup2cns" /> + <param name="min_coverage" value="8" /> + <param name="min_reads2" value="2" /> + <param name="min_avg_qual" value="15" /> + <param name="min_var_freq" value="0.01" /> + <param name="min_freq_for_hom" value="0.75" /> + <param name="p_value" value="0.99" /> + <param name="strand_filter" value="no" /> + <param name="sample_names" value="" /> + <output name="output" file="varscan_mpileup_result1.vcf" lines_diff="0" /> + </test> + </tests> + + <help> +**VarScan Overview** + +VarScan_ performs variant detection for massively parallel sequencing data, such as exome, WGS, and transcriptome data. +It calls variants from a mpileup dataset and produces a VCF 4.1. Full documentation is available online_. + +This tool detects variants from pileups. + +.. _VarScan: http://dkoboldt.github.io/varscan/ +.. _online: http://dkoboldt.github.io/varscan/using-varscan.html + +**Input** + +:: + + mpileup file - The SAMtools mpileup file + + +**Output** + +VarScan produces a VCF 4.1 dataset as output. + + </help> + <expand macro="citations" /> +</tool> |