Mercurial > repos > greg > cfsan_snp_pipeline_merge_sites
changeset 0:201984e0cab2 draft
Uploaded
| author | greg |
|---|---|
| date | Fri, 13 Oct 2023 14:20:19 +0000 |
| parents | |
| children | 1013b32b325a |
| files | .shed.yml cfsan_snp_pipeline_merge_sites.xml macros.xml snp_wind.py test-data/input1.vcf test-data/input2.vcf test-data/input3.vcf test-data/input4.vcf test-data/output.tabular |
| diffstat | 9 files changed, 573 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.shed.yml Fri Oct 13 14:20:19 2023 +0000 @@ -0,0 +1,11 @@ +name: cfsan_snp_pipeline_merge_sites +owner: greg +description: Combine the SNP positions across all samples into a single unified SNP list + file identifying the positions and sample names where SNPs were called. +long_description: Combine the SNP positions across all samples into a single unified SNP list +file identifying the positions and sample names where SNPs were called. +categories: +- Metagenomics +remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/snp_pipeline/cfsan_snp_pipeline_merge_sites +homepage_url: https://github.com/gregvonkuster/galaxy_tools +type: unrestricted
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cfsan_snp_pipeline_merge_sites.xml Fri Oct 13 14:20:19 2023 +0000 @@ -0,0 +1,59 @@ +<tool id="cfsan_snp_pipeline_merge_sites" name="CFSAN SNP Pipeline: merge sites" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>from multiple samples</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +python '$__tool_directory__/snp_wind.py' ./ +#if str($input_type_cond.input_type) == 'single': + -n '$input_vcf.element_identifier' + -f '$input_vcf' +#else: + #for $input_vcf in $input_vcf_collection + -n '$input_vcf.element_identifier' + -f '$input_vcf' + #end for +#end if +-p 'var.fit.vcf' > ./file +&& cfsan_snp_pipeline merge_sites -v 4 -n 'var.fit.vcf' ./file ./filtered_snps -o '$output' + ]]></command> + <inputs> + <expand macro="input_type_cond"/> + </inputs> + <outputs> + <data name="output" format="tabular"/> + </outputs> + <tests> + <test> + <param name="input_type" value="collection"/> + <param name="input_vcf_collection"> + <collection type="list"> + <element name="input1" value="input1.vcf" ftype="vcf"/> + <element name="input2" value="input2.vcf" ftype="vcf"/> + <element name="input3" value="input3.vcf" ftype="vcf"/> + <element name="input4" value="input4.vcf" ftype="vcf"/> + </collection> + </param> + <output name="output" value="output.tabular"/> + </test> + </tests> + <help><![CDATA[ +**What it does** + +Combine the SNP positions across all samples into a single unified SNP list +file identifing the positions and sample names where SNPs were called. + +**Optional parameters** + + * **force** - Force processing even when result file already exists and is newer than inputs (default: False) + * **vcfname** - File name of the VCF files which must exist in each of the sample directories (default: var.flt.vcf) + * **maxsnps** - Exclude samples having more than this maximum allowed number of SNPs. Set to -1 to disable this function (default: -1) + +**More information** + +CFSAN SNP Pipeline `merge sites documentation <https://snp-pipeline.readthedocs.io/en/latest/cmd_ref.html#merge-sites>`_ + ]]></help> + <expand macro="citations"/> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Oct 13 14:20:19 2023 +0000 @@ -0,0 +1,31 @@ +<macros> + <token name="@TOOL_VERSION@">2.2.1</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">21.01</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">snp-pipeline</requirement> + <requirement type="package" version="3.6.8">python</requirement> + </requirements> + </xml> + <xml name="input_type_cond"> + <conditional name="input_type_cond"> + <param name="input_type" type="select" label="Choose the category for the files to be analyzed"> + <option value="single" selected="true">Single files</option> + <option value="collection">Collection of files</option> + </param> + <when value="single"> + <param name="input_vcf" type="data" format="vcf" label="VCF file"/> + </when> + <when value="collection"> + <param name="input_vcf_collection" type="data_collection" format="vcf" collection_type="list" label="Collection of VCF files"/> + </when> + </conditional> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.7717/peerj-cs.20</citation> + </citations> + </xml> +</macros> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snp_wind.py Fri Oct 13 14:20:19 2023 +0000 @@ -0,0 +1,42 @@ +#!/usr/bin/env python + +import argparse +import os +from os.path import join as j +from itertools import zip_longest + + +def setup(base_dir, names=[], fwds=[], revs=[], extension='vcf', pattern="{name}.{orient}.{ext}"): + if fwds and revs and names and len(fwds) != len(revs) != len(names): + raise ValueError('number of forward reads must equal number of reverse reads and names') + elif len(fwds) != len(names) or not fwds or not names: + raise ValueError('number of forward reads must equal number of names') + with open(j(base_dir, 'snp-unwind.sh'), 'w') as unwind: + for i, (name, fwd, rev) in enumerate(zip_longest(names, fwds, revs)): + dir = j(base_dir, str(i)) + sample_dir = j(dir, name) + os.makedirs(sample_dir) + target_f = j(sample_dir, pattern.format(name=name, orient=1, ext=extension)) + if rev: + target_r = j(sample_dir, pattern.format(name=name, orient=2, ext=extension)) + os.symlink(fwd, target_f) + if rev: + os.symlink(rev, target_r) + print(sample_dir) + if rev: + unwind.write('unlink {}\n'.format(target_r)) + unwind.write('unlink {}\n'.format(target_f)) + unwind.write('rmdir {}\n'.format(sample_dir)) + unwind.write('rmdir {}\n'.format(dir)) + + +if __name__ == '__main__': + parser = argparse.ArgumentParser(description="set up vcf symlink directories for snp-pipeline") + parser.add_argument('base_dir') + parser.add_argument('-n', dest='names', type=str, action='append', default=[]) + parser.add_argument('-f', dest='fwds', type=str, action='append', default=[]) + parser.add_argument('-r', dest='revs', type=str, action='append', default=[]) + parser.add_argument('-e', dest='extension', default='vcf') + parser.add_argument('-p', dest='pattern', default='{name}.{orient}.{ext}') + params = parser.parse_args() + setup(**vars(params))
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input1.vcf Fri Oct 13 14:20:19 2023 +0000 @@ -0,0 +1,71 @@ +##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 +gi|9626243|ref|NC_001416.1| 403 . G A . PASS ADP=26;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:146:27:26:0:26:100%:2.0165E-15:0:31:0:0:12:14 +gi|9626243|ref|NC_001416.1| 753 . G A . PASS ADP=24;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:129:25:24:0:23:100%:1.2146E-13:0:27:0:0:15:8 +gi|9626243|ref|NC_001416.1| 1079 . T C . PASS ADP=25;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:135:26:25:0:24:100%:3.101E-14:0:26:0:0:9:15 +gi|9626243|ref|NC_001416.1| 1540 . A G . PASS ADP=22;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:123:24:22:0:22:100%:4.7526E-13:0:24:0:0:13:9 +gi|9626243|ref|NC_001416.1| 1804 . G C . PASS ADP=23;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:129:23:23:0:23:100%:1.2146E-13:0:28:0:0:11:12 +gi|9626243|ref|NC_001416.1| 2123 . G C . PASS ADP=23;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:129:24:23:0:23:100%:1.2146E-13:0:27:0:0:10:13 +gi|9626243|ref|NC_001416.1| 3351 . C G . PASS ADP=22;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:123:24:22:0:22:100%:4.7526E-13:0:28:0:0:10:12 +gi|9626243|ref|NC_001416.1| 3656 . T G . PASS ADP=23;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:129:25:23:0:23:100%:1.2146E-13:0:25:0:0:12:11 +gi|9626243|ref|NC_001416.1| 4977 . G A . PASS ADP=22;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:123:25:22:0:22:100%:4.7526E-13:0:27:0:0:10:12 +gi|9626243|ref|NC_001416.1| 5482 . G A . PASS ADP=17;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:93:18:17:0:17:100%:4.2852E-10:0:28:0:0:8:9 +gi|9626243|ref|NC_001416.1| 5516 . T A . PASS ADP=13;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:70:16:13:0:13:100%:9.6148E-8:0:23:0:0:7:6 +gi|9626243|ref|NC_001416.1| 5800 . G A . PASS ADP=13;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:70:19:13:0:13:100%:9.6148E-8:0:26:0:0:4:9 +gi|9626243|ref|NC_001416.1| 6824 . A C . PASS ADP=18;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:99:19:18:0:18:100%:1.1019E-10:0:26:0:0:10:8 +gi|9626243|ref|NC_001416.1| 7897 . G A . PASS ADP=23;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:129:26:23:0:23:100%:1.2146E-13:0:25:0:0:11:12 +gi|9626243|ref|NC_001416.1| 9175 . A G . PASS ADP=22;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:123:22:22:0:22:100%:4.7526E-13:0:28:0:0:8:14 +gi|9626243|ref|NC_001416.1| 12717 . G C . PASS ADP=25;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:135:29:25:0:24:100%:3.101E-14:0:28:0:0:10:14 +gi|9626243|ref|NC_001416.1| 12795 . C T . PASS ADP=26;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:146:27:26:0:26:100%:2.0165E-15:0:29:0:0:16:10 +gi|9626243|ref|NC_001416.1| 12959 . T G . PASS ADP=21;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:117:22:21:0:21:100%:1.8578E-12:0:25:0:0:13:8 +gi|9626243|ref|NC_001416.1| 16654 . C G . PASS ADP=23;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:129:24:23:0:23:100%:1.2146E-13:0:26:0:0:14:9 +gi|9626243|ref|NC_001416.1| 16715 . T G . PASS ADP=18;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:99:19:18:0:18:100%:1.1019E-10:0:25:0:0:8:10 +gi|9626243|ref|NC_001416.1| 18598 . C G . PASS ADP=22;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:123:25:22:0:22:100%:4.7526E-13:0:24:0:0:12:10 +gi|9626243|ref|NC_001416.1| 19469 . G T . PASS ADP=18;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:99:21:18:0:18:100%:1.1019E-10:0:28:0:0:11:7 +gi|9626243|ref|NC_001416.1| 20099 . C T . PASS ADP=28;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:158:28:28:0:28:100%:1.3074E-16:0:29:0:0:14:14 +gi|9626243|ref|NC_001416.1| 21110 . T G . PASS ADP=16;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:87:18:16:0:16:100%:1.6637E-9:0:26:0:0:5:11 +gi|9626243|ref|NC_001416.1| 23362 . T A . PASS ADP=11;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:58:14:11:0:11:100%:1.4176E-6:0:26:0:0:3:8 +gi|9626243|ref|NC_001416.1| 24319 . G T . PASS ADP=18;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:99:19:18:0:18:100%:1.1019E-10:0:26:0:0:7:11 +gi|9626243|ref|NC_001416.1| 24766 . G A . PASS ADP=17;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:93:19:17:0:17:100%:4.2852E-10:0:24:0:0:6:11 +gi|9626243|ref|NC_001416.1| 27790 . A C . PASS ADP=18;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:93:20:18:0:17:100%:4.2852E-10:0:26:0:0:6:11 +gi|9626243|ref|NC_001416.1| 29891 . G C . PASS ADP=20;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:111:21:20:0:20:100%:7.2544E-12:0:26:0:0:9:11 +gi|9626243|ref|NC_001416.1| 31551 . A G . PASS ADP=15;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:81:16:15:0:15:100%:6.4467E-9:0:25:0:0:7:8 +gi|9626243|ref|NC_001416.1| 32086 . T A . PASS ADP=15;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:69:17:15:1:14:93.33%:1.0315E-7:33:28:1:0:7:7 +gi|9626243|ref|NC_001416.1| 33000 . C T . PASS ADP=17;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:93:18:17:0:17:100%:4.2852E-10:0:26:0:0:7:10 +gi|9626243|ref|NC_001416.1| 33591 . T G . PASS ADP=30;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:170:30:30:0:30:100%:8.4556E-18:0:26:0:0:16:14 +gi|9626243|ref|NC_001416.1| 34370 . A G . PASS ADP=22;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:117:23:22:0:21:100%:1.8578E-12:0:26:0:0:10:11 +gi|9626243|ref|NC_001416.1| 34812 . A C . PASS ADP=16;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:81:16:16:0:15:100%:6.4467E-9:0:26:0:0:11:4 +gi|9626243|ref|NC_001416.1| 34920 . T C . PASS ADP=15;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:81:16:15:0:15:100%:6.4467E-9:0:23:0:0:9:6 +gi|9626243|ref|NC_001416.1| 35148 . C A . PASS ADP=16;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:87:16:16:0:16:100%:1.6637E-9:0:26:0:0:10:6 +gi|9626243|ref|NC_001416.1| 36010 . C T . PASS ADP=9;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:46:9:9:0:9:100%:2.0568E-5:0:26:0:0:0:9 +gi|9626243|ref|NC_001416.1| 37208 . G C . PASS ADP=19;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:105:19:19:0:19:100%:2.8292E-11:0:29:0:0:8:11 +gi|9626243|ref|NC_001416.1| 38165 . T C . PASS ADP=27;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:152:29:27:0:27:100%:5.1363E-16:0:23:0:0:17:10 +gi|9626243|ref|NC_001416.1| 39485 . A C . PASS ADP=20;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:111:20:20:0:20:100%:7.2544E-12:0:29:0:0:10:10 +gi|9626243|ref|NC_001416.1| 40457 . T C . PASS ADP=27;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:138:28:27:1:26:96.3%:1.4382E-14:24:25:1:0:11:15 +gi|9626243|ref|NC_001416.1| 42439 . A C . PASS ADP=24;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:135:28:24:0:24:100%:3.101E-14:0:26:0:0:16:8 +gi|9626243|ref|NC_001416.1| 43306 . T G . PASS ADP=32;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:176:33:32:0:31:100%:2.1486E-18:0:27:0:0:11:20 +gi|9626243|ref|NC_001416.1| 46237 . G A . PASS ADP=27;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:152:27:27:0:27:100%:5.1363E-16:0:26:0:0:12:15 +gi|9626243|ref|NC_001416.1| 47893 . G A . PASS ADP=23;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:129:28:23:0:23:100%:1.2146E-13:0:25:0:0:12:11 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input2.vcf Fri Oct 13 14:20:19 2023 +0000 @@ -0,0 +1,69 @@ +##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 +gi|9626243|ref|NC_001416.1| 2599 . C A . PASS ADP=24;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:135:25:24:0:24:100%:3.101E-14:0:26:0:0:8:16 +gi|9626243|ref|NC_001416.1| 3678 . C T . PASS ADP=16;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:75:19:16:1:15:93.75%:2.8282E-8:17:26:1:0:8:7 +gi|9626243|ref|NC_001416.1| 5142 . C G . PASS ADP=17;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:93:18:17:0:17:100%:4.2852E-10:0:27:0:0:4:13 +gi|9626243|ref|NC_001416.1| 5336 . G T . PASS ADP=8;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:41:8:8:0:8:100%:7.77E-5:0:31:0:0:1:7 +gi|9626243|ref|NC_001416.1| 5994 . A T . PASS ADP=21;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:117:21:21:0:21:100%:1.8578E-12:0:24:0:0:10:11 +gi|9626243|ref|NC_001416.1| 6535 . C A . PASS ADP=19;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:99:22:19:0:18:100%:1.1019E-10:0:27:0:0:6:12 +gi|9626243|ref|NC_001416.1| 7424 . G T . PASS ADP=21;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:117:25:21:0:21:100%:1.8578E-12:0:26:0:0:13:8 +gi|9626243|ref|NC_001416.1| 10127 . G A . PASS ADP=26;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:146:32:26:0:26:100%:2.0165E-15:0:26:0:0:14:12 +gi|9626243|ref|NC_001416.1| 11782 . A G . PASS ADP=16;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:87:17:16:0:16:100%:1.6637E-9:0:28:0:0:7:9 +gi|9626243|ref|NC_001416.1| 13264 . C T . PASS ADP=22;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:123:23:22:0:22:100%:4.7526E-13:0:26:0:0:14:8 +gi|9626243|ref|NC_001416.1| 13542 . C G . PASS ADP=23;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:123:26:23:0:22:95.65%:4.7526E-13:0:29:0:0:14:8 +gi|9626243|ref|NC_001416.1| 13952 . G C . PASS ADP=31;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:176:33:31:0:31:100%:2.1486E-18:0:26:0:0:13:18 +gi|9626243|ref|NC_001416.1| 15715 . G C . PASS ADP=21;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:117:24:21:0:21:100%:1.8578E-12:0:28:0:0:15:6 +gi|9626243|ref|NC_001416.1| 15967 . A T . PASS ADP=24;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:129:28:24:0:23:100%:1.2146E-13:0:24:0:0:13:10 +gi|9626243|ref|NC_001416.1| 17142 . G A . PASS ADP=23;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:129:27:23:0:23:100%:1.2146E-13:0:29:0:0:12:11 +gi|9626243|ref|NC_001416.1| 17311 . G C . PASS ADP=33;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:188:35:33:0:33:100%:1.3852E-19:0:26:0:0:14:19 +gi|9626243|ref|NC_001416.1| 17854 . G T . PASS ADP=19;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:105:20:19:0:19:100%:2.8292E-11:0:26:0:0:5:14 +gi|9626243|ref|NC_001416.1| 18420 . G T . PASS ADP=17;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:93:18:17:0:17:100%:4.2852E-10:0:26:0:0:9:8 +gi|9626243|ref|NC_001416.1| 18652 . G T . PASS ADP=23;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:129:25:23:0:23:100%:1.2146E-13:0:25:0:0:13:10 +gi|9626243|ref|NC_001416.1| 19208 . A C . PASS ADP=16;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:87:17:16:0:16:100%:1.6637E-9:0:26:0:0:8:8 +gi|9626243|ref|NC_001416.1| 20367 . G C . PASS ADP=30;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:170:32:30:0:30:100%:8.4556E-18:0:27:0:0:19:11 +gi|9626243|ref|NC_001416.1| 21320 . T C . PASS ADP=23;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:129:25:23:0:23:100%:1.2146E-13:0:29:0:0:11:12 +gi|9626243|ref|NC_001416.1| 22220 . A C . PASS ADP=27;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:152:28:27:0:27:100%:5.1363E-16:0:23:0:0:17:10 +gi|9626243|ref|NC_001416.1| 22747 . G A . PASS ADP=18;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:99:19:18:0:18:100%:1.1019E-10:0:28:0:0:6:12 +gi|9626243|ref|NC_001416.1| 23457 . A C . PASS ADP=19;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:99:20:19:0:18:100%:1.1019E-10:0:27:0:0:11:7 +gi|9626243|ref|NC_001416.1| 25005 . A C . PASS ADP=11;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:58:12:11:0:11:100%:1.4176E-6:0:26:0:0:5:6 +gi|9626243|ref|NC_001416.1| 25158 . A C . PASS ADP=20;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:111:22:20:0:20:100%:7.2544E-12:0:27:0:0:10:10 +gi|9626243|ref|NC_001416.1| 25645 . C G . PASS ADP=24;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:135:26:24:0:24:100%:3.101E-14:0:26:0:0:10:14 +gi|9626243|ref|NC_001416.1| 26173 . G C . PASS ADP=21;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:117:21:21:0:21:100%:1.8578E-12:0:26:0:0:10:11 +gi|9626243|ref|NC_001416.1| 27661 . T C . PASS ADP=23;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:123:25:23:0:22:100%:4.7526E-13:0:28:0:0:14:8 +gi|9626243|ref|NC_001416.1| 28045 . G T . PASS ADP=25;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:141:25:25:0:25:100%:7.9107E-15:0:29:0:0:13:12 +gi|9626243|ref|NC_001416.1| 28362 . T C . PASS ADP=20;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:111:22:20:0:20:100%:7.2544E-12:0:24:0:0:12:8 +gi|9626243|ref|NC_001416.1| 29411 . T C . PASS ADP=28;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:158:31:28:0:28:100%:1.3074E-16:0:28:0:0:13:15 +gi|9626243|ref|NC_001416.1| 30125 . A G . PASS ADP=21;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:117:21:21:0:21:100%:1.8578E-12:0:29:0:0:11:10 +gi|9626243|ref|NC_001416.1| 34137 . T G . PASS ADP=33;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:182:34:33:0:32:100%:5.4567E-19:0:25:0:0:17:15 +gi|9626243|ref|NC_001416.1| 35907 . G T . PASS ADP=31;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:164:32:31:0:29:100%:3.3259E-17:0:27:0:0:18:11 +gi|9626243|ref|NC_001416.1| 38575 . A C . PASS ADP=21;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:117:21:21:0:21:100%:1.8578E-12:0:28:0:0:10:11 +gi|9626243|ref|NC_001416.1| 39206 . T C . PASS ADP=18;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:93:20:18:0:17:100%:4.2852E-10:0:24:0:0:7:10 +gi|9626243|ref|NC_001416.1| 39484 . C A . PASS ADP=18;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:99:20:18:0:18:100%:1.1019E-10:0:24:0:0:11:7 +gi|9626243|ref|NC_001416.1| 43470 . G T . PASS ADP=21;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:117:25:21:0:21:100%:1.8578E-12:0:29:0:0:12:9 +gi|9626243|ref|NC_001416.1| 44134 . T C . PASS ADP=21;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:111:22:21:0:20:100%:7.2544E-12:0:25:0:0:12:8 +gi|9626243|ref|NC_001416.1| 44413 . G T . PASS ADP=31;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:176:32:31:0:31:100%:2.1486E-18:0:26:0:0:13:18 +gi|9626243|ref|NC_001416.1| 45364 . A C . PASS ADP=27;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:141:27:27:0:25:96.15%:7.9107E-15:0:27:0:0:16:9 +gi|9626243|ref|NC_001416.1| 47425 . T C . PASS ADP=18;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:93:19:18:0:17:100%:4.2852E-10:0:26:0:0:11:6 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input3.vcf Fri Oct 13 14:20:19 2023 +0000 @@ -0,0 +1,63 @@ +##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 +gi|9626243|ref|NC_001416.1| 2439 . C T . PASS ADP=14;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:76:16:14:0:14:100%:2.4927E-8:0:26:0:0:6:8 +gi|9626243|ref|NC_001416.1| 3648 . C T . PASS ADP=24;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:129:28:24:0:23:100%:1.2146E-13:0:26:0:0:12:11 +gi|9626243|ref|NC_001416.1| 5462 . C T . PASS ADP=21;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:105:24:21:0:19:100%:2.8292E-11:0:25:0:0:16:3 +gi|9626243|ref|NC_001416.1| 7668 . A C . PASS ADP=15;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:81:17:15:0:15:100%:6.4467E-9:0:26:0:0:5:10 +gi|9626243|ref|NC_001416.1| 8420 . T C . PASS ADP=31;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:176:32:31:0:31:100%:2.1486E-18:0:26:0:0:21:10 +gi|9626243|ref|NC_001416.1| 9919 . A G . PASS ADP=23;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:129:24:23:0:23:100%:1.2146E-13:0:28:0:0:14:9 +gi|9626243|ref|NC_001416.1| 10264 . G T . PASS ADP=21;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:117:24:21:0:21:100%:1.8578E-12:0:26:0:0:9:12 +gi|9626243|ref|NC_001416.1| 11066 . G C . PASS ADP=18;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:99:20:18:0:18:100%:1.1019E-10:0:25:0:0:6:12 +gi|9626243|ref|NC_001416.1| 12070 . C T . PASS ADP=10;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:52:11:10:0:10:100%:5.4125E-6:0:22:0:0:7:3 +gi|9626243|ref|NC_001416.1| 12970 . A G . PASS ADP=24;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:135:26:24:0:24:100%:3.101E-14:0:25:0:0:13:11 +gi|9626243|ref|NC_001416.1| 13107 . C A . PASS ADP=12;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:64:16:12:0:12:100%:3.698E-7:0:24:0:0:7:5 +gi|9626243|ref|NC_001416.1| 13971 . G C . PASS ADP=25;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:141:27:25:0:25:100%:7.9107E-15:0:27:0:0:12:13 +gi|9626243|ref|NC_001416.1| 15384 . T G . PASS ADP=23;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:129:24:23:0:23:100%:1.2146E-13:0:26:0:0:15:8 +gi|9626243|ref|NC_001416.1| 16070 . C A . PASS ADP=18;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:93:22:18:0:17:94.44%:4.2852E-10:0:25:0:0:13:4 +gi|9626243|ref|NC_001416.1| 18151 . A T . PASS ADP=21;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:117:22:21:0:21:100%:1.8578E-12:0:26:0:0:10:11 +gi|9626243|ref|NC_001416.1| 18989 . G T . PASS ADP=29;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:164:30:29:0:29:100%:3.3259E-17:0:28:0:0:13:16 +gi|9626243|ref|NC_001416.1| 19448 . C A . PASS ADP=19;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:92:20:19:1:18:94.74%:5.6585E-10:28:26:1:0:7:11 +gi|9626243|ref|NC_001416.1| 20079 . C G . PASS ADP=34;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:194:36:34:0:34:100%:3.5146E-20:0:25:0:0:18:16 +gi|9626243|ref|NC_001416.1| 20289 . T A . PASS ADP=21;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:117:23:21:0:21:100%:1.8578E-12:0:27:0:0:6:15 +gi|9626243|ref|NC_001416.1| 21653 . G C . PASS ADP=20;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:111:22:20:0:20:100%:7.2544E-12:0:29:0:0:14:6 +gi|9626243|ref|NC_001416.1| 24930 . A C . PASS ADP=23;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:129:26:23:0:23:100%:1.2146E-13:0:28:0:0:11:12 +gi|9626243|ref|NC_001416.1| 26728 . A T . PASS ADP=24;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:135:25:24:0:24:100%:3.101E-14:0:26:0:0:12:12 +gi|9626243|ref|NC_001416.1| 27412 . C G . PASS ADP=13;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:70:15:13:0:13:100%:9.6148E-8:0:25:0:0:5:8 +gi|9626243|ref|NC_001416.1| 27834 . C A . PASS ADP=15;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:76:16:15:0:14:100%:2.4927E-8:0:23:0:0:9:5 +gi|9626243|ref|NC_001416.1| 29435 . T A . PASS ADP=13;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:70:18:13:0:13:100%:9.6148E-8:0:28:0:0:6:7 +gi|9626243|ref|NC_001416.1| 30757 . T A . PASS ADP=20;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:111:24:20:0:20:100%:7.2544E-12:0:28:0:0:7:13 +gi|9626243|ref|NC_001416.1| 30890 . G A . PASS ADP=17;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:87:18:17:0:16:100%:1.6637E-9:0:26:0:0:7:9 +gi|9626243|ref|NC_001416.1| 31328 . G C . PASS ADP=20;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:111:21:20:0:20:100%:7.2544E-12:0:27:0:0:9:11 +gi|9626243|ref|NC_001416.1| 32660 . C A . PASS ADP=16;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:87:17:16:0:16:100%:1.6637E-9:0:25:0:0:10:6 +gi|9626243|ref|NC_001416.1| 33865 . T G . PASS ADP=26;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:146:28:26:0:26:100%:2.0165E-15:0:27:0:0:13:13 +gi|9626243|ref|NC_001416.1| 35802 . G C . PASS ADP=25;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:141:28:25:0:25:100%:7.9107E-15:0:24:0:0:11:14 +gi|9626243|ref|NC_001416.1| 36169 . G C . PASS ADP=13;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:70:15:13:0:13:100%:9.6148E-8:0:26:0:0:4:9 +gi|9626243|ref|NC_001416.1| 37519 . G C . PASS ADP=13;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:70:13:13:0:13:100%:9.6148E-8:0:30:0:0:6:7 +gi|9626243|ref|NC_001416.1| 37898 . C G . PASS ADP=24;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:135:27:24:0:24:100%:3.101E-14:0:26:0:0:8:16 +gi|9626243|ref|NC_001416.1| 38073 . A C . PASS ADP=24;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:129:25:24:0:23:100%:1.2146E-13:0:25:0:0:17:6 +gi|9626243|ref|NC_001416.1| 39003 . T C . PASS ADP=16;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:87:17:16:0:16:100%:1.6637E-9:0:25:0:0:8:8 +gi|9626243|ref|NC_001416.1| 41448 . A G . PASS ADP=19;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:105:21:19:0:19:100%:2.8292E-11:0:23:0:0:7:12 +gi|9626243|ref|NC_001416.1| 46842 . G C . PASS ADP=26;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:141:28:26:0:25:100%:7.9107E-15:0:26:0:0:16:9 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input4.vcf Fri Oct 13 14:20:19 2023 +0000 @@ -0,0 +1,62 @@ +##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 +gi|9626243|ref|NC_001416.1| 550 . G A . PASS ADP=23;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:129:26:23:0:23:100%:1.2146E-13:0:27:0:0:14:9 +gi|9626243|ref|NC_001416.1| 586 . C G . PASS ADP=25;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:129:27:25:0:23:100%:1.2146E-13:0:27:0:0:16:7 +gi|9626243|ref|NC_001416.1| 1019 . C T . PASS ADP=20;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:111:22:20:0:20:100%:7.2544E-12:0:25:0:0:7:13 +gi|9626243|ref|NC_001416.1| 1620 . G A . PASS ADP=17;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:93:19:17:0:17:100%:4.2852E-10:0:26:0:0:7:10 +gi|9626243|ref|NC_001416.1| 1650 . G C . PASS ADP=25;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:141:26:25:0:25:100%:7.9107E-15:0:26:0:0:10:15 +gi|9626243|ref|NC_001416.1| 1788 . A T . PASS ADP=16;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:87:16:16:0:16:100%:1.6637E-9:0:26:0:0:9:7 +gi|9626243|ref|NC_001416.1| 2452 . A T . PASS ADP=21;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:103:23:21:1:20:95.24%:4.0873E-11:33:27:1:0:13:7 +gi|9626243|ref|NC_001416.1| 3063 . G A . PASS ADP=20;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:105:22:20:0:19:100%:2.8292E-11:0:28:0:0:9:10 +gi|9626243|ref|NC_001416.1| 5818 . G T . PASS ADP=22;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:117:23:22:0:21:95.45%:1.8578E-12:0:25:0:0:10:11 +gi|9626243|ref|NC_001416.1| 6296 . T A . PASS ADP=24;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:129:26:24:0:23:100%:1.2146E-13:0:28:0:0:12:11 +gi|9626243|ref|NC_001416.1| 8938 . T A . PASS ADP=29;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:164:29:29:0:29:100%:3.3259E-17:0:23:0:0:17:12 +gi|9626243|ref|NC_001416.1| 9234 . C T . PASS ADP=19;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:105:21:19:0:19:100%:2.8292E-11:0:26:0:0:9:10 +gi|9626243|ref|NC_001416.1| 10421 . G T . PASS ADP=17;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:93:18:17:0:17:100%:4.2852E-10:0:28:0:0:7:10 +gi|9626243|ref|NC_001416.1| 10568 . C T . PASS ADP=20;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:111:21:20:0:20:100%:7.2544E-12:0:28:0:0:10:10 +gi|9626243|ref|NC_001416.1| 11128 . T A . PASS ADP=24;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:135:25:24:0:24:100%:3.101E-14:0:28:0:0:10:14 +gi|9626243|ref|NC_001416.1| 12876 . G C . PASS ADP=18;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:99:19:18:0:18:100%:1.1019E-10:0:26:0:0:7:11 +gi|9626243|ref|NC_001416.1| 13647 . C T . PASS ADP=15;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:81:17:15:0:15:100%:6.4467E-9:0:26:0:0:9:6 +gi|9626243|ref|NC_001416.1| 18188 . T C . PASS ADP=25;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:141:31:25:0:25:100%:7.9107E-15:0:23:0:0:14:11 +gi|9626243|ref|NC_001416.1| 18210 . C G . PASS ADP=27;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:152:29:27:0:27:100%:5.1363E-16:0:24:0:0:14:13 +gi|9626243|ref|NC_001416.1| 22357 . G A . PASS ADP=21;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:117:21:21:0:21:100%:1.8578E-12:0:25:0:0:11:10 +gi|9626243|ref|NC_001416.1| 24043 . C A . PASS ADP=15;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:81:15:15:0:15:100%:6.4467E-9:0:27:0:0:7:8 +gi|9626243|ref|NC_001416.1| 26972 . A T . PASS ADP=21;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:103:22:21:1:20:95.24%:4.0873E-11:35:26:1:0:11:9 +gi|9626243|ref|NC_001416.1| 27539 . A C . PASS ADP=11;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:58:11:11:0:11:100%:1.4176E-6:0:30:0:0:5:6 +gi|9626243|ref|NC_001416.1| 27722 . C A . PASS ADP=25;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:141:26:25:0:25:100%:7.9107E-15:0:24:0:0:15:10 +gi|9626243|ref|NC_001416.1| 27825 . A G . PASS ADP=20;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:111:22:20:0:20:100%:7.2544E-12:0:27:0:0:13:7 +gi|9626243|ref|NC_001416.1| 29265 . T C . PASS ADP=24;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:129:28:24:0:23:100%:1.2146E-13:0:26:0:0:7:16 +gi|9626243|ref|NC_001416.1| 31363 . C G . PASS ADP=8;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:41:9:8:0:8:100%:7.77E-5:0:27:0:0:7:1 +gi|9626243|ref|NC_001416.1| 33612 . C A . PASS ADP=18;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:93:19:18:0:17:100%:4.2852E-10:0:25:0:0:7:10 +gi|9626243|ref|NC_001416.1| 36642 . T C . PASS ADP=15;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:81:17:15:0:15:100%:6.4467E-9:0:28:0:0:2:13 +gi|9626243|ref|NC_001416.1| 37387 . A T . PASS ADP=14;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:76:15:14:0:14:100%:2.4927E-8:0:27:0:0:7:7 +gi|9626243|ref|NC_001416.1| 40835 . T C . PASS ADP=21;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:117:25:21:0:21:100%:1.8578E-12:0:27:0:0:14:7 +gi|9626243|ref|NC_001416.1| 40984 . A G . PASS ADP=22;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:117:22:22:0:21:100%:1.8578E-12:0:24:0:0:12:9 +gi|9626243|ref|NC_001416.1| 41064 . T G . PASS ADP=19;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:99:22:19:0:18:94.74%:1.1019E-10:0:25:0:0:7:11 +gi|9626243|ref|NC_001416.1| 41954 . T C . PASS ADP=22;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:123:23:22:0:22:100%:4.7526E-13:0:27:0:0:10:12 +gi|9626243|ref|NC_001416.1| 44201 . G C . PASS ADP=22;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:117:25:22:0:21:100%:1.8578E-12:0:27:0:0:14:7 +gi|9626243|ref|NC_001416.1| 45409 . C G . PASS ADP=21;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:117:21:21:0:21:100%:1.8578E-12:0:26:0:0:8:13 +gi|9626243|ref|NC_001416.1| 46283 . C G . PASS ADP=20;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:111:22:20:0:20:100%:7.2544E-12:0:28:0:0:10:10 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.tabular Fri Oct 13 14:20:19 2023 +0000 @@ -0,0 +1,165 @@ +gi|9626243|ref|NC_001416.1| 403 1 input1 +gi|9626243|ref|NC_001416.1| 550 1 input4 +gi|9626243|ref|NC_001416.1| 586 1 input4 +gi|9626243|ref|NC_001416.1| 753 1 input1 +gi|9626243|ref|NC_001416.1| 1019 1 input4 +gi|9626243|ref|NC_001416.1| 1079 1 input1 +gi|9626243|ref|NC_001416.1| 1540 1 input1 +gi|9626243|ref|NC_001416.1| 1620 1 input4 +gi|9626243|ref|NC_001416.1| 1650 1 input4 +gi|9626243|ref|NC_001416.1| 1788 1 input4 +gi|9626243|ref|NC_001416.1| 1804 1 input1 +gi|9626243|ref|NC_001416.1| 2123 1 input1 +gi|9626243|ref|NC_001416.1| 2439 1 input3 +gi|9626243|ref|NC_001416.1| 2452 1 input4 +gi|9626243|ref|NC_001416.1| 2599 1 input2 +gi|9626243|ref|NC_001416.1| 3063 1 input4 +gi|9626243|ref|NC_001416.1| 3351 1 input1 +gi|9626243|ref|NC_001416.1| 3648 1 input3 +gi|9626243|ref|NC_001416.1| 3656 1 input1 +gi|9626243|ref|NC_001416.1| 3678 1 input2 +gi|9626243|ref|NC_001416.1| 4977 1 input1 +gi|9626243|ref|NC_001416.1| 5142 1 input2 +gi|9626243|ref|NC_001416.1| 5336 1 input2 +gi|9626243|ref|NC_001416.1| 5462 1 input3 +gi|9626243|ref|NC_001416.1| 5482 1 input1 +gi|9626243|ref|NC_001416.1| 5516 1 input1 +gi|9626243|ref|NC_001416.1| 5800 1 input1 +gi|9626243|ref|NC_001416.1| 5818 1 input4 +gi|9626243|ref|NC_001416.1| 5994 1 input2 +gi|9626243|ref|NC_001416.1| 6296 1 input4 +gi|9626243|ref|NC_001416.1| 6535 1 input2 +gi|9626243|ref|NC_001416.1| 6824 1 input1 +gi|9626243|ref|NC_001416.1| 7424 1 input2 +gi|9626243|ref|NC_001416.1| 7668 1 input3 +gi|9626243|ref|NC_001416.1| 7897 1 input1 +gi|9626243|ref|NC_001416.1| 8420 1 input3 +gi|9626243|ref|NC_001416.1| 8938 1 input4 +gi|9626243|ref|NC_001416.1| 9175 1 input1 +gi|9626243|ref|NC_001416.1| 9234 1 input4 +gi|9626243|ref|NC_001416.1| 9919 1 input3 +gi|9626243|ref|NC_001416.1| 10127 1 input2 +gi|9626243|ref|NC_001416.1| 10264 1 input3 +gi|9626243|ref|NC_001416.1| 10421 1 input4 +gi|9626243|ref|NC_001416.1| 10568 1 input4 +gi|9626243|ref|NC_001416.1| 11066 1 input3 +gi|9626243|ref|NC_001416.1| 11128 1 input4 +gi|9626243|ref|NC_001416.1| 11782 1 input2 +gi|9626243|ref|NC_001416.1| 12070 1 input3 +gi|9626243|ref|NC_001416.1| 12717 1 input1 +gi|9626243|ref|NC_001416.1| 12795 1 input1 +gi|9626243|ref|NC_001416.1| 12876 1 input4 +gi|9626243|ref|NC_001416.1| 12959 1 input1 +gi|9626243|ref|NC_001416.1| 12970 1 input3 +gi|9626243|ref|NC_001416.1| 13107 1 input3 +gi|9626243|ref|NC_001416.1| 13264 1 input2 +gi|9626243|ref|NC_001416.1| 13542 1 input2 +gi|9626243|ref|NC_001416.1| 13647 1 input4 +gi|9626243|ref|NC_001416.1| 13952 1 input2 +gi|9626243|ref|NC_001416.1| 13971 1 input3 +gi|9626243|ref|NC_001416.1| 15384 1 input3 +gi|9626243|ref|NC_001416.1| 15715 1 input2 +gi|9626243|ref|NC_001416.1| 15967 1 input2 +gi|9626243|ref|NC_001416.1| 16070 1 input3 +gi|9626243|ref|NC_001416.1| 16654 1 input1 +gi|9626243|ref|NC_001416.1| 16715 1 input1 +gi|9626243|ref|NC_001416.1| 17142 1 input2 +gi|9626243|ref|NC_001416.1| 17311 1 input2 +gi|9626243|ref|NC_001416.1| 17854 1 input2 +gi|9626243|ref|NC_001416.1| 18151 1 input3 +gi|9626243|ref|NC_001416.1| 18188 1 input4 +gi|9626243|ref|NC_001416.1| 18210 1 input4 +gi|9626243|ref|NC_001416.1| 18420 1 input2 +gi|9626243|ref|NC_001416.1| 18598 1 input1 +gi|9626243|ref|NC_001416.1| 18652 1 input2 +gi|9626243|ref|NC_001416.1| 18989 1 input3 +gi|9626243|ref|NC_001416.1| 19208 1 input2 +gi|9626243|ref|NC_001416.1| 19448 1 input3 +gi|9626243|ref|NC_001416.1| 19469 1 input1 +gi|9626243|ref|NC_001416.1| 20079 1 input3 +gi|9626243|ref|NC_001416.1| 20099 1 input1 +gi|9626243|ref|NC_001416.1| 20289 1 input3 +gi|9626243|ref|NC_001416.1| 20367 1 input2 +gi|9626243|ref|NC_001416.1| 21110 1 input1 +gi|9626243|ref|NC_001416.1| 21320 1 input2 +gi|9626243|ref|NC_001416.1| 21653 1 input3 +gi|9626243|ref|NC_001416.1| 22220 1 input2 +gi|9626243|ref|NC_001416.1| 22357 1 input4 +gi|9626243|ref|NC_001416.1| 22747 1 input2 +gi|9626243|ref|NC_001416.1| 23362 1 input1 +gi|9626243|ref|NC_001416.1| 23457 1 input2 +gi|9626243|ref|NC_001416.1| 24043 1 input4 +gi|9626243|ref|NC_001416.1| 24319 1 input1 +gi|9626243|ref|NC_001416.1| 24766 1 input1 +gi|9626243|ref|NC_001416.1| 24930 1 input3 +gi|9626243|ref|NC_001416.1| 25005 1 input2 +gi|9626243|ref|NC_001416.1| 25158 1 input2 +gi|9626243|ref|NC_001416.1| 25645 1 input2 +gi|9626243|ref|NC_001416.1| 26173 1 input2 +gi|9626243|ref|NC_001416.1| 26728 1 input3 +gi|9626243|ref|NC_001416.1| 26972 1 input4 +gi|9626243|ref|NC_001416.1| 27412 1 input3 +gi|9626243|ref|NC_001416.1| 27539 1 input4 +gi|9626243|ref|NC_001416.1| 27661 1 input2 +gi|9626243|ref|NC_001416.1| 27722 1 input4 +gi|9626243|ref|NC_001416.1| 27790 1 input1 +gi|9626243|ref|NC_001416.1| 27825 1 input4 +gi|9626243|ref|NC_001416.1| 27834 1 input3 +gi|9626243|ref|NC_001416.1| 28045 1 input2 +gi|9626243|ref|NC_001416.1| 28362 1 input2 +gi|9626243|ref|NC_001416.1| 29265 1 input4 +gi|9626243|ref|NC_001416.1| 29411 1 input2 +gi|9626243|ref|NC_001416.1| 29435 1 input3 +gi|9626243|ref|NC_001416.1| 29891 1 input1 +gi|9626243|ref|NC_001416.1| 30125 1 input2 +gi|9626243|ref|NC_001416.1| 30757 1 input3 +gi|9626243|ref|NC_001416.1| 30890 1 input3 +gi|9626243|ref|NC_001416.1| 31328 1 input3 +gi|9626243|ref|NC_001416.1| 31363 1 input4 +gi|9626243|ref|NC_001416.1| 31551 1 input1 +gi|9626243|ref|NC_001416.1| 32086 1 input1 +gi|9626243|ref|NC_001416.1| 32660 1 input3 +gi|9626243|ref|NC_001416.1| 33000 1 input1 +gi|9626243|ref|NC_001416.1| 33591 1 input1 +gi|9626243|ref|NC_001416.1| 33612 1 input4 +gi|9626243|ref|NC_001416.1| 33865 1 input3 +gi|9626243|ref|NC_001416.1| 34137 1 input2 +gi|9626243|ref|NC_001416.1| 34370 1 input1 +gi|9626243|ref|NC_001416.1| 34812 1 input1 +gi|9626243|ref|NC_001416.1| 34920 1 input1 +gi|9626243|ref|NC_001416.1| 35148 1 input1 +gi|9626243|ref|NC_001416.1| 35802 1 input3 +gi|9626243|ref|NC_001416.1| 35907 1 input2 +gi|9626243|ref|NC_001416.1| 36010 1 input1 +gi|9626243|ref|NC_001416.1| 36169 1 input3 +gi|9626243|ref|NC_001416.1| 36642 1 input4 +gi|9626243|ref|NC_001416.1| 37208 1 input1 +gi|9626243|ref|NC_001416.1| 37387 1 input4 +gi|9626243|ref|NC_001416.1| 37519 1 input3 +gi|9626243|ref|NC_001416.1| 37898 1 input3 +gi|9626243|ref|NC_001416.1| 38073 1 input3 +gi|9626243|ref|NC_001416.1| 38165 1 input1 +gi|9626243|ref|NC_001416.1| 38575 1 input2 +gi|9626243|ref|NC_001416.1| 39003 1 input3 +gi|9626243|ref|NC_001416.1| 39206 1 input2 +gi|9626243|ref|NC_001416.1| 39484 1 input2 +gi|9626243|ref|NC_001416.1| 39485 1 input1 +gi|9626243|ref|NC_001416.1| 40457 1 input1 +gi|9626243|ref|NC_001416.1| 40835 1 input4 +gi|9626243|ref|NC_001416.1| 40984 1 input4 +gi|9626243|ref|NC_001416.1| 41064 1 input4 +gi|9626243|ref|NC_001416.1| 41448 1 input3 +gi|9626243|ref|NC_001416.1| 41954 1 input4 +gi|9626243|ref|NC_001416.1| 42439 1 input1 +gi|9626243|ref|NC_001416.1| 43306 1 input1 +gi|9626243|ref|NC_001416.1| 43470 1 input2 +gi|9626243|ref|NC_001416.1| 44134 1 input2 +gi|9626243|ref|NC_001416.1| 44201 1 input4 +gi|9626243|ref|NC_001416.1| 44413 1 input2 +gi|9626243|ref|NC_001416.1| 45364 1 input2 +gi|9626243|ref|NC_001416.1| 45409 1 input4 +gi|9626243|ref|NC_001416.1| 46237 1 input1 +gi|9626243|ref|NC_001416.1| 46283 1 input4 +gi|9626243|ref|NC_001416.1| 46842 1 input3 +gi|9626243|ref|NC_001416.1| 47425 1 input2 +gi|9626243|ref|NC_001416.1| 47893 1 input1