| Previous changeset 57:d3095ad12f24 (2020-11-06) Next changeset 59:49d672730d3e (2024-06-17) |
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Commit message:
planemo upload |
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modified:
0_index_ref.xml.old 1_map_reads.xml 2_call_sites.xml 3_filter_regions.xml 4_merge_sites.xml 5_call_consensus.xml 6_merge_vcfs.xml 7_smp_matrix.xml CFSAN_SNP_Pipeline.ga snp-filter.py snp-pipeline.xml.old test-data/metrics.tsv test-data/reference/lambda_virus.fasta test-data/reference/lambda_virus.fasta.fai test-data/reference/reference.1.bt2 test-data/reference/reference.2.bt2 test-data/reference/reference.3.bt2 test-data/reference/reference.4.bt2 test-data/reference/reference.rev.1.bt2 test-data/reference/reference.rev.2.bt2 test-data/reference/reference.tar.gz test-data/referenceSNP.fasta test-data/samples/sample1/consensus.fasta test-data/samples/sample1/consensus.vcf test-data/samples/sample1/consensus_preserved.vcf test-data/samples/sample1/duplicate_reads_metrics.txt test-data/samples/sample1/metrics test-data/samples/sample1/reads.sam test-data/samples/sample1/reads.sorted.bam test-data/samples/sample1/reads.sorted.deduped.bam test-data/samples/sample1/reads.unsorted.bam test-data/samples/sample1/sample1_1.fastq test-data/samples/sample1/sample1_1.fastq.gz test-data/samples/sample1/sample1_2.fastq test-data/samples/sample1/sample1_2.fastq.gz test-data/samples/sample1/var.flt.vcf test-data/samples/sample1/var.flt_removed.vcf test-data/samples/sample2/consensus.fasta test-data/samples/sample2/consensus.vcf test-data/samples/sample2/consensus_preserved.fasta test-data/samples/sample2/consensus_preserved.vcf test-data/samples/sample2/duplicate_reads_metrics.txt test-data/samples/sample2/metrics test-data/samples/sample2/reads.all.pileup test-data/samples/sample2/reads.sam test-data/samples/sample2/reads.sorted.bam test-data/samples/sample2/reads.sorted.deduped.bam test-data/samples/sample2/reads.unsorted.bam test-data/samples/sample2/sample2_1.fastq test-data/samples/sample2/sample2_2.fastq test-data/samples/sample2/var.flt.vcf test-data/samples/sample2/var.flt_preserved.vcf test-data/samples/sample2/var.flt_removed.vcf test-data/samples/sample3/consensus.fasta test-data/samples/sample3/consensus.vcf test-data/samples/sample3/consensus_preserved.fasta test-data/samples/sample3/consensus_preserved.vcf test-data/samples/sample3/duplicate_reads_metrics.txt test-data/samples/sample3/metrics test-data/samples/sample3/reads.all.pileup test-data/samples/sample3/reads.sam test-data/samples/sample3/reads.sorted.bam test-data/samples/sample3/reads.sorted.deduped.bam test-data/samples/sample3/reads.unsorted.bam test-data/samples/sample3/sample3_1.fastq test-data/samples/sample3/sample3_2.fastq test-data/samples/sample3/var.flt.vcf test-data/samples/sample3/var.flt_preserved.vcf test-data/samples/sample3/var.flt_removed.vcf test-data/samples/sample4/consensus.fasta test-data/samples/sample4/consensus.vcf test-data/samples/sample4/consensus_preserved.fasta test-data/samples/sample4/consensus_preserved.vcf test-data/samples/sample4/duplicate_reads_metrics.txt test-data/samples/sample4/metrics test-data/samples/sample4/reads.all.pileup test-data/samples/sample4/reads.sam test-data/samples/sample4/reads.sorted.bam test-data/samples/sample4/reads.sorted.deduped.bam test-data/samples/sample4/reads.unsorted.bam test-data/samples/sample4/sample4_1.fastq test-data/samples/sample4/sample4_2.fastq test-data/samples/sample4/var.flt.vcf test-data/samples/sample4/var.flt_preserved.vcf test-data/samples/sample4/var.flt_removed.vcf test-data/snp_distance_matrix.tsv test-data/snp_distance_pairwise.tsv test-data/snpma.fasta test-data/snpma.vcf tool-data/all_fasta.loc.sample tool_data_table_conf.xml.sample |
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added:
Mambaforge-Linux-x86_64.sh test-data/samples/sample1/var.flt_preserved.vcf |
| 1_map_reads.xml |
| diff -r d3095ad12f24 -r d53281e6edae 1_map_reads.xml |
| 1_map_reads.xml |
| --- a/1_map_reads.xml Fri Nov 06 12:50:48 2020 -0500 +++ b/1_map_reads.xml Mon Jun 17 02:57:10 2024 -0400 @@ -1,10 +1,11 @@ <tool id="map_reads" name="1. Map Reads" version="1.0.1" profile="16.10"> <description>to index, or lookup cached alignment</description> <requirements> - <requirement type="package" version="1.0.6">bzip2</requirement> - <requirement type="package" version="2.3.5">bowtie2</requirement> + <container type="docker">quay.io/biocontainers/mulled-v2-d736175c8392ecaa2a26c372df9ad15b78f8d5b8:d59a38d618c862df52cf9dae223ed9d93ed7225b-0</container> + <requirement type="package" version="1.0.8">bzip2</requirement> + <requirement type="package" version="2.4.5">bowtie2</requirement> <requirement type="package" version="1.9.134">boto3</requirement> - <requirement type="package" version="3.6.8">python</requirement> + <!-- <requirement type="package" version="3.6.8">python</requirement> --> </requirements> <command detect_errors="exit_code"><![CDATA[ export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && |
| 2_call_sites.xml |
| diff -r d3095ad12f24 -r d53281e6edae 2_call_sites.xml |
| 2_call_sites.xml |
| --- a/2_call_sites.xml Fri Nov 06 12:50:48 2020 -0500 +++ b/2_call_sites.xml Mon Jun 17 02:57:10 2024 -0400 @@ -1,13 +1,14 @@ <tool id="call_sites" name="2. Call Sites" version="1.0.1" profile="16.10"> <description>of high-confidence SNPs, or lookup cached sitecall</description> <requirements> - <requirement type="package" version="2.3.5">bowtie2</requirement> + <container type="docker">quay.io/biocontainers/mulled-v2-e518cb713b80020daa244e2ce559c37edb42dcde:5cb90165033bd74a97d0a807f439cf4b1aaabb89-0</container> + <requirement type="package" version="2.4.5">bowtie2</requirement> <requirement type="package" version="1.9">samtools</requirement> - <requirement type="package" version="1.0.6">bzip2</requirement> - <requirement type="package">picard</requirement> - <requirement type="package">varscan</requirement> + <requirement type="package" version="1.0.8">bzip2</requirement> + <requirement type="package" version="2.27.4">picard</requirement> + <requirement type="package" version="2.4.4">varscan</requirement> <requirement type="package" version="1.9.134">boto3</requirement> - <requirement type="package" version="3.6.8">python</requirement> + <!-- <requirement type="package" version="3.6.8">python</requirement> --> </requirements> <command detect_errors="exit_code"><![CDATA[ export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && |
| 3_filter_regions.xml |
| diff -r d3095ad12f24 -r d53281e6edae 3_filter_regions.xml |
| 3_filter_regions.xml |
| --- a/3_filter_regions.xml Fri Nov 06 12:50:48 2020 -0500 +++ b/3_filter_regions.xml Mon Jun 17 02:57:10 2024 -0400 @@ -1,11 +1,12 @@ <tool id="filter_regions" name="3. Filter SNP Regions" version="1.0.1" profile="16.10"> <description>based on SNP location, or lookup cached filtered sitecall</description> <requirements> + <container type="docker">quay.io/biocontainers/mulled-v2-b387422e12acd8cf2ba9f5f1b0f12c36f93c00b7:b1c910a35786ca780412af4d314af0670e08604f-0</container> <requirement type="package" version="1.9">samtools</requirement> - <requirement type="package" version="1.0.6">bzip2</requirement> - <requirement type="package" version="2.0.2">snp-pipeline</requirement> + <requirement type="package" version="1.0.8">bzip2</requirement> + <requirement type="package" version="2.2.1">snp-pipeline</requirement> <requirement type="package" version="1.9.134">boto3</requirement> - <requirement type="package" version="3.6.8">python</requirement> + <!-- <requirement type="package" version="3.6.8">python</requirement> --> </requirements> <command detect_errors="exit_code"><![CDATA[ export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && |
| 4_merge_sites.xml |
| diff -r d3095ad12f24 -r d53281e6edae 4_merge_sites.xml |
| 4_merge_sites.xml |
| --- a/4_merge_sites.xml Fri Nov 06 12:50:48 2020 -0500 +++ b/4_merge_sites.xml Mon Jun 17 02:57:10 2024 -0400 @@ -1,11 +1,12 @@ <tool id="merge_sites" name="4. Merge Sites" version="1.0.1" profile="16.10"> <description>from multiple samples</description> <requirements> - <requirement type="package" version="2.3.5">bowtie2</requirement> + <container type="docker">quay.io/biocontainers/mulled-v2-a9689be5d4f7dc232fcd76f2f32bef2b80afcb49:0560aee94873e022862623c7766c9634a09b9513-0</container> + <requirement type="package" version="2.4.5">bowtie2</requirement> <requirement type="package" version="1.9">samtools</requirement> - <requirement type="package" version="1.0.6">bzip2</requirement> - <requirement type="package" version="2.0.2">snp-pipeline</requirement> - <requirement type="package" version="3.6.8">python</requirement> + <requirement type="package" version="1.0.8">bzip2</requirement> + <requirement type="package" version="2.2.1">snp-pipeline</requirement> + <!-- <requirement type="package" version="3.6.8">python</requirement> --> </requirements> <command detect_errors="exit_code"><![CDATA[ export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && @@ -32,7 +33,7 @@ <element name="sample4" value="samples/sample4/var.flt_preserved.vcf" ftype="fastqsanger" /> </collection> </param> - <!-- <output name="snplist" value="snplist.txt" /> --> + <output name="snplist" value="snplist.txt" /> </test> </tests> <help><![CDATA[ |
| 5_call_consensus.xml |
| diff -r d3095ad12f24 -r d53281e6edae 5_call_consensus.xml |
| 5_call_consensus.xml |
| --- a/5_call_consensus.xml Fri Nov 06 12:50:48 2020 -0500 +++ b/5_call_consensus.xml Mon Jun 17 02:57:10 2024 -0400 @@ -1,10 +1,11 @@ <tool id="call_consensus" name="5. Call consensus SNPs" version="1.0.1" profile="16.10"> <description>for a sample, or lookup cached consensus SNP calls</description> <requirements> - <requirement type="package" version="1.0.6">bzip2</requirement> - <requirement type="package" version="2.0.2">snp-pipeline</requirement> + <container type="docker">quay.io/biocontainers/mulled-v2-fe715cf36e5a6063362b28e50f1f4a1a767770d5:8f94687b7d8826f1473b7e97df0cea2a960b35bf-0</container> + <requirement type="package" version="1.0.8">bzip2</requirement> + <requirement type="package" version="2.2.1">snp-pipeline</requirement> <requirement type="package" version="1.9.134">boto3</requirement> - <requirement type="package" version="3.6.8">python</requirement> + <!-- <requirement type="package" version="3.6.8">python</requirement> --> </requirements> <command detect_errors="exit_code"><![CDATA[ export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && |
| 6_merge_vcfs.xml |
| diff -r d3095ad12f24 -r d53281e6edae 6_merge_vcfs.xml |
| 6_merge_vcfs.xml |
| --- a/6_merge_vcfs.xml Fri Nov 06 12:50:48 2020 -0500 +++ b/6_merge_vcfs.xml Mon Jun 17 02:57:10 2024 -0400 @@ -1,12 +1,13 @@ <tool id="merge_vcfs" name="6. Merge VCFs" version="1.0.1" profile="16.10"> <description>into a multi-sample VCF with consensus SNPs</description> <requirements> + <container type="docker">quay.io/biocontainers/mulled-v2-72d480da2f80e0804df2fc75273988c6dba1648d:f354c444b518b0ada8e031aa2984346e2f5d8837-0</container> <requirement type="package" version="1.9">bcftools</requirement> - <requirement type="package" version="1.0.6">bzip2</requirement> - <requirement type="package" version="2.0.2">snp-pipeline</requirement> - <requirement type="package" version="0.2.5">tabix</requirement> + <requirement type="package" version="1.0.8">bzip2</requirement> + <requirement type="package" version="2.2.1">snp-pipeline</requirement> + <requirement type="package" version="0.2.6">tabix</requirement> <requirement type="package" version="1.9">htslib</requirement> - <requirement type="package" version="3.6.8">python</requirement> + <!-- <requirement type="package" version="3.6.8">python</requirement> --> </requirements> <command detect_errors="exit_code"><![CDATA[ export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && |
| 7_smp_matrix.xml |
| diff -r d3095ad12f24 -r d53281e6edae 7_smp_matrix.xml |
| 7_smp_matrix.xml |
| --- a/7_smp_matrix.xml Fri Nov 06 12:50:48 2020 -0500 +++ b/7_smp_matrix.xml Mon Jun 17 02:57:10 2024 -0400 @@ -1,11 +1,12 @@ <tool id="snp_matrix" name="7. Create a SNP matrix" version="1.0.1" profile="16.10"> <description>and associated distance metrics</description> <requirements> + <container type="docker">quay.io/biocontainers/mulled-v2-d2e223d7ac457e81243657cd7ae8336bd1c16e8e:81b350b3fbf165cbf5db53022037a2657a660701-0</container> <requirement type="package" version="1.9">bcftools</requirement> - <requirement type="package" version="1.0.6">bzip2</requirement> - <requirement type="package" version="2.0.2">snp-pipeline</requirement> - <requirement type="package" version="0.2.5">tabix</requirement> - <requirement type="package" version="3.6.8">python</requirement> + <requirement type="package" version="1.0.8">bzip2</requirement> + <requirement type="package" version="2.2.1">snp-pipeline</requirement> + <requirement type="package" version="0.2.6">tabix</requirement> + <!-- <requirement type="package" version="3.6.8">python</requirement> --> </requirements> <command detect_errors="exit_code"><![CDATA[ export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" && |
| Mambaforge-Linux-x86_64.sh |
| diff -r d3095ad12f24 -r d53281e6edae Mambaforge-Linux-x86_64.sh |
| Mambaforge-Linux-x86_64.sh |
| Binary file Mambaforge-Linux-x86_64.sh has changed |
| test-data/samples/sample1/reads.sam |
| diff -r d3095ad12f24 -r d53281e6edae test-data/samples/sample1/reads.sam |
| test-data/samples/sample1/reads.sam |
| --- a/test-data/samples/sample1/reads.sam Fri Nov 06 12:50:48 2020 -0500 +++ b/test-data/samples/sample1/reads.sam Mon Jun 17 02:57:10 2024 -0400 @@ -1,6 +1,6 @@ @HD VN:1.0 SO:unsorted @SQ SN:gi|9626243|ref|NC_001416.1| LN:48502 -@PG ID:bowtie2 PN:bowtie2 VN:2.3.3.1 CL:"/usr/local/bin/bowtie2-align-s --wrapper basic-0 --reorder -X 1000 -p 2 -x reference/lambda_virus -1 samples/sample1/sample1_1.fastq -2 samples/sample1/sample1_2.fastq" +@PG ID:bowtie2 PN:bowtie2 VN:2.3.5.1 CL:"/home/chet/miniconda3/envs/mulled-v1-3aaacfa732fb5a9a4edb89d75dc27c600fe12abcc61b59ef7e28f09be834e1ba/bin/bowtie2-align-s --wrapper basic-0 -q -x ./reference -p 1 --reorder -X 1000 -1 ./forward.gz -2 ./reverse.gz" r1 83 gi|9626243|ref|NC_001416.1| 16266 42 97M = 16003 -360 GCAATACAGCGGTATCTGGGACGGAACGTTTAAACCGGCATACAGCAACAACATGGCCTGGCGTCTGTGGGATTTGCTGACCCATCCGCGCTACGGC *5:441C0)"E,A%72$9-"1%A:8%-0<80-;6H8%7643HB>9*;8BED.D#.2?44:4'5)0<6F6F1*C71A.D;G0G<2<9.6/B:3")?4' AS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:61T11A23 YS:i:0 YT:Z:CP r1 163 gi|9626243|ref|NC_001416.1| 16003 42 58M = 16266 360 GTGGTGATGGGTAACCTGCCGCCGCGCCCGTTTAATATCCGGATGCGCAGGATGACGC );A!/,6B:8=(*2GE1FGA>0/,?>),%.,/3+@D(C=<53!$H"HE-$79*HD?4< AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:58 YS:i:-6 YT:Z:CP r2 83 gi|9626243|ref|NC_001416.1| 35315 42 60M = 35108 -267 CCTGTTTCTCTGCGNGACGTTCGCGGCGGCGTNTTTGTGCATCCATCTGGATTCTCCTGT E*CD88'0F(71,0A>GA4:@@+CB%@/8369*H2%!"0CE/BE<:4F)3&1BF&:*7#2 AS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14C17G27 YS:i:-6 YT:Z:CP |
| test-data/samples/sample1/var.flt_preserved.vcf |
| diff -r d3095ad12f24 -r d53281e6edae test-data/samples/sample1/var.flt_preserved.vcf |
| test-data/samples/sample1/var.flt_preserved.vcf |
| --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samples/sample1/var.flt_preserved.vcf Mon Jun 17 02:57:10 2024 -0400 @@ -0,0 +1,61 @@ +##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"> +##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)"> +##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"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1 +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| 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..BQ: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| 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 |
| test-data/snpma.vcf |
| diff -r d3095ad12f24 -r d53281e6edae test-data/snpma.vcf |
| test-data/snpma.vcf |
| --- a/test-data/snpma.vcf Fri Nov 06 12:50:48 2020 -0500 +++ b/test-data/snpma.vcf Mon Jun 17 02:57:10 2024 -0400 @@ -19,8 +19,8 @@ ##FILTER=<ID=StrBias0,Description="Fraction of variant supporting reads below 0.00 on one strand"> ##FILTER=<ID=Region,Description="Position is in dense region of snps or near the end of the contig."> ##contig=<ID=gi|9626243|ref|NC_001416.1|> -##bcftools_mergeVersion=1.3.1+htslib-1.3.1 -##bcftools_mergeCommand=merge -o ./snpma.vcf --merge all --info-rules NS:sum ./tmp.vcf.PYaZFQ/sample1.vcf.gz ./tmp.vcf.PYaZFQ/sample2.vcf.gz ./tmp.vcf.PYaZFQ/sample3.vcf.gz ./tmp.vcf.PYaZFQ/sample4.vcf.gz +##bcftools_mergeVersion=1.9+htslib-1.9 +##bcftools_mergeCommand=merge -o snpma.vcf --merge all --info-rules NS:sum tmp.vcf.3imm9gjk/sample1.vcf.gz tmp.vcf.3imm9gjk/sample2.vcf.gz tmp.vcf.3imm9gjk/sample3.vcf.gz tmp.vcf.3imm9gjk/sample4.vcf.gz; Date=Mon Aug 1 12:20:35 2022 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2 sample3 sample4 gi|9626243|ref|NC_001416.1| 403 . G A . PASS NS=4 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 1:27:0:27:0:0:13:14:PASS 0:24:24:0:11:13:0:0:PASS 0:26:26:0:13:13:0:0:PASS 0:15:15:0:11:4:0:0:PASS gi|9626243|ref|NC_001416.1| 550 . G A . PASS NS=4 GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT 0:22:21:1:13:8:0:1:PASS 0:26:26:0:14:12:0:0:PASS 0:29:29:0:13:16:0:0:PASS 1:26:0:26:0:0:14:12:PASS |