# HG changeset patch # User iuc # Date 1573077777 18000 # Node ID ef2c525bd8cdb0888578c3b3e81c6ba50005c4cf # Parent 156b60c1530f92581c179ac4b4ddecc869f52131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8" diff -r 156b60c1530f -r ef2c525bd8cd freebayes.xml --- a/freebayes.xml Wed Oct 25 08:29:45 2017 -0400 +++ b/freebayes.xml Wed Nov 06 17:02:57 2019 -0500 @@ -1,4 +1,4 @@ - + bayesian genetic variant detector macros.xml @@ -77,26 +77,29 @@ ## Outputs --vcf './vcf_output/part_\$i.vcf' + ## Coverage + #if str($coverage_options.coverage_options_selector) == "set": + @COVERAGE@ + #end if + ##advanced options #if str( $options_type.options_type_selector ) == "simple": #pass #elif str( $options_type.options_type_selector ) == "simple_w_filters": --standard-filters - --min-coverage ${options_type.min_coverage} #elif str( $options_type.options_type_selector ) == "naive": --haplotype-length 0 --min-alternate-count 1 - --min-alternate-fraction 0 + --min-alternate-fraction 0.05 --pooled-continuous --report-monomorphic #elif str( $options_type.options_type_selector ) == "naive_w_filters": --haplotype-length 0 --min-alternate-count 1 - --min-alternate-fraction 0 + --min-alternate-fraction 0.05 --pooled-continuous --report-monomorphic --standard-filters - --min-coverage ${options_type.min_coverage} #elif str( $options_type.options_type_selector ) == "full": #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set': ${options_type.optional_inputs.report_monomorphic} @@ -189,7 +192,6 @@ --read-snp-limit ${options_type.input_filters.mismatch_filters.read_snp_limit} #end if - --min-coverage ${options_type.input_filters.min_coverage} --min-alternate-qsum ${options_type.input_filters.min_alternate_qsum} #end if @@ -305,6 +307,17 @@ + + + + + + + + + + @@ -315,6 +328,7 @@ + @@ -439,7 +453,7 @@ label="Allow haplotype calls with contiguous embedded matches of up to (nucleotides)" /> - - @@ -504,7 +518,6 @@ label="Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position" /> - @@ -585,17 +598,9 @@ - - - - - - - - - - - + + + @@ -622,6 +627,7 @@ + @@ -631,6 +637,7 @@ + @@ -644,8 +651,38 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + :- Limit analysis to the specified region, 0-base coordinates, + end_position not included (same as BED format). + Either '-' or '..' maybe used as a separator. + --samples FILE Limit analysis to samples listed (one per line) in the FILE. + By default FreeBayes will analyze all samples in its input + BAM files. + --populations FILE Each line of FILE should list a sample and a population which + it is part of. The population-based bayesian inference model + will then be partitioned on the basis of the populations. + --cnv-map FILE Read a copy number map from the BED file FILE, which has + either a sample-level ploidy: + sample_name copy_number + or a region-specific format: + seq_name start end sample_name copy_number + ... for each region in each sample which does not have the + default copy number as set by --ploidy. These fields can be delimited + by space or tab. + +**Output**:: + + --vcf FILE Output VCF-format results to FILE. (default: stdout) + --gvcf Write gVCF output, which indicates coverage in uncalled regions. + --gvcf-chunk NUM When writing gVCF output emit a record for every NUM bases. + --gvcf-dont-use-chunk When writing the gVCF output emit a record for all bases if + set to "true" , will also route an int to --gvcf-chunk + similar to --output-mode EMIT_ALL_SITES from GATK + --variant-input VCF Use variants reported in VCF file as input to the algorithm. + Variants in this file will included in the output even if + there is not enough support in the data to pass input filters. + --only-use-input-alleles Only provide variant calls and genotype likelihoods for sites + and alleles which are provided in the VCF input, and provide + output in the VCF for all input alleles, not just those which + have support in the data. + --haplotype-basis-alleles VCF When specified, only variant alleles provided in this input + VCF will be used for the construction of complex or haplotype + alleles. + --report-all-haplotype-alleles At sites where genotypes are made over haplotype alleles, + provide information about all alleles in output, not only + those which are called. + --report-monomorphic Report even loci which appear to be monomorphic, and report all + considered alleles, even those which are not in called genotypes. + Loci which do not have any potential alternates have '.' for ALT. + --pvar N Report sites if the probability that there is a polymorphism + at the site is greater than N. default: 0.0. Note that post- + filtering is generally recommended over the use of this parameter. + --strict-vcf Generate strict VCF format (FORMAT/GQ will be an int) + +**Population model**:: + + --theta N The expected mutation rate or pairwise nucleotide diversity + among the population under analysis. This serves as the + single parameter to the Ewens Sampling Formula prior model + default: 0.001 + --ploidy N Sets the default ploidy for the analysis to N. default: 2 + --pooled-discrete Assume that samples result from pooled sequencing. + Model pooled samples using discrete genotypes across pools. + When using this flag, set --ploidy to the number of + alleles in each sample or use the --cnv-map to define + per-sample ploidy. + --pooled-continuous Output all alleles which pass input filters, regardles of + genotyping outcome or model. + +**Reference allele**:: + + --use-reference-allele This flag includes the reference allele in the analysis as + if it is another sample from the same population. + --reference-quality MQ,BQ Assign mapping quality of MQ to the reference allele at each + site and base quality of BQ. default: 100,60 + +**Allele scope**:: + + --use-best-n-alleles N Evaluate only the best N SNP alleles, ranked by sum of + supporting quality scores. (Set to 0 to use all; default: all) + --max-complex-gap + --haplotype-length N Allow haplotype calls with contiguous embedded matches of up + to this length. Set N=-1 to disable clumping. (default: 3) + --min-repeat-size When assembling observations across repeats, require the total repeat + length at least this many bp. (default: 5) + --min-repeat-entropy N To detect interrupted repeats, build across sequence until it has + entropy > N bits per bp. Set to 0 to turn off. (default: 1) + --no-partial-observations Exclude observations which do not fully span the dynamically-determined + detection window. (default, use all observations, dividing partial + support across matching haplotypes when generating haplotypes.) + +**Indel realignment**:: + + --dont-left-align-indels Turn off left-alignment of indels, which is enabled by default. + +**Input filters**:: + + --use-duplicate-reads Include duplicate-marked alignments in the analysis. + default: exclude duplicates marked as such in alignments + --min-mapping-quality Q Exclude alignments from analysis if they have a mapping + quality less than Q. default: 1 + --min-base-quality Q Exclude alleles from analysis if their supporting base + quality is less than Q. default: 0 + --min-supporting-allele-qsum Q Consider any allele in which the sum of qualities of supporting + observations is at least Q. default: 0 + --min-supporting-mapping-qsum Q Consider any allele in which and the sum of mapping qualities of + supporting reads is at least Q. default: 0 + --mismatch-base-quality-threshold Q Count mismatches toward --read-mismatch-limit if the base + quality of the mismatch is >= Q. default: 10 + --read-mismatch-limit N Exclude reads with more than N mismatches where each mismatch + has base quality >= mismatch-base-quality-threshold. + default: ~unbounded + --read-max-mismatch-fraction N Exclude reads with more than N [0,1] fraction of mismatches where + each mismatch has base quality >= mismatch-base-quality-threshold + default: 1.0 + --read-snp-limit N Exclude reads with more than N base mismatches, ignoring gaps + with quality >= mismatch-base-quality-threshold. + default: ~unbounded + --read-indel-limit N Exclude reads with more than N separate gaps. + default: ~unbounded + --standard-filters Use stringent input base and mapping quality filters + Equivalent to -m 30 -q 20 -R 0 -S 0 + --min-alternate-fraction N Require at least this fraction of observations supporting + an alternate allele within a single individual in the + in order to evaluate the position. default: 0.05 + --min-alternate-count N Require at least this count of observations supporting + an alternate allele within a single individual in order + to evaluate the position. default: 2 + --min-alternate-qsum N Require at least this sum of quality of observations supporting + an alternate allele within a single individual in order + to evaluate the position. default: 0 + --min-alternate-total N Require at least this count of observations supporting + an alternate allele within the total population in order + to use the allele in analysis. default: 1 + --min-coverage N Require at least this coverage to process a site. default: 0 + --limit-coverage N Downsample per-sample coverage to this level if greater than this coverage. + default: no limit + --skip-coverage N Skip processing of alignments overlapping positions with coverage >N. + This filters sites above this coverage, but will also reduce data nearby. + default: no limit + +**Population priors**:: + + --no-population-priors Equivalent to --pooled-discrete --hwe-priors-off and removal of + Ewens Sampling Formula component of priors. + +**Mappability priors**:: + + --hwe-priors-off Disable estimation of the probability of the combination + arising under HWE given the allele frequency as estimated + by observation frequency. + --binomial-obs-priors-off Disable incorporation of prior expectations about observations. + Uses read placement probability, strand balance probability, + and read position (5'-3') probability. + --allele-balance-priors-off Disable use of aggregate probability of observation balance between alleles + as a component of the priors. + +**Genotype likelihoods**:: + + --observation-bias FILE Read length-dependent allele observation biases from FILE. + The format is [length] [alignment efficiency relative to reference] + where the efficiency is 1 if there is no relative observation bias. + --base-quality-cap Q Limit estimated observation quality by capping base quality at Q. + --prob-contamination F An estimate of contamination to use for all samples. default: 10e-9 + --legacy-gls Use legacy (polybayes equivalent) genotype likelihood calculations + --contamination-estimates FILE A file containing per-sample estimates of contamination, such as + those generated by VerifyBamID. The format should be: + sample p(read=R|genotype=AR) p(read=A|genotype=AA) + Sample '*' can be used to set default contamination estimates. + +**Algorithmic features**:: + + --report-genotype-likelihood-max Report genotypes using the maximum-likelihood estimate provided + from genotype likelihoods. + --genotyping-max-iterations N Iterate no more than N times during genotyping step. default: 1000. + --genotyping-max-banddepth N Integrate no deeper than the Nth best genotype by likelihood when + genotyping. default: 6. + --posterior-integration-limits N,M Integrate all genotype combinations in our posterior space + which include no more than N samples with their Mth best + data likelihood. default: 1,3. + --exclude-unobserved-genotypes Skip sample genotypings for which the sample has no supporting reads. + --genotype-variant-threshold N Limit posterior integration to samples where the second-best + genotype likelihood is no more than log(N) from the highest + genotype likelihood for the sample. default: ~unbounded + --use-mapping-quality Use mapping quality of alleles when calculating data likelihoods. + --harmonic-indel-quality Use a weighted sum of base qualities around an indel, scaled by the + distance from the indel. By default use a minimum BQ in flanking sequence. + --read-dependence-factor N Incorporate non-independence of reads by scaling successive + observations by this factor during data likelihood + calculations. default: 0.9 + --genotype-qualities Calculate the marginal probability of genotypes and report as GQ in + each sample field in the VCF output. + +------ + **Acknowledgments** The initial version of the wrapper was produced by Dan Blankenberg and upgraded by Anton Nekrutenko. TNG was developed by Bjoern Gruening. +]]> diff -r 156b60c1530f -r ef2c525bd8cd leftalign.xml --- a/leftalign.xml Wed Oct 25 08:29:45 2017 -0400 +++ b/leftalign.xml Wed Nov 06 17:02:57 2019 -0500 @@ -1,5 +1,5 @@ - + indels in BAM datasets macros.xml @@ -40,7 +40,7 @@ - + diff -r 156b60c1530f -r ef2c525bd8cd macros.xml --- a/macros.xml Wed Oct 25 08:29:45 2017 -0400 +++ b/macros.xml Wed Nov 06 17:02:57 2019 -0500 @@ -1,9 +1,9 @@ - 1.1.0.46 + 1.3.1 freebayes - samtools + samtools @@ -43,7 +43,14 @@ + + --min-coverage ${coverage_options.min_coverage} + --skip-coverage ${coverage_options.skip_coverage} + --limit-coverage ${coverage_options.limit_coverage} + - + + + diff -r 156b60c1530f -r ef2c525bd8cd test-data/freebayes-hxb2-test5.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/freebayes-hxb2-test5.vcf Wed Nov 06 17:02:57 2019 -0500 @@ -0,0 +1,74 @@ +##fileformat=VCFv4.2 +##fileDate=20191101 +##source=freeBayes v1.3.1-dirty +##reference=localref.fa +##contig= +##phasing=none +##commandline="freebayes --region K03455:0..9719 --bam b_0.bam --fasta-reference localref.fa --vcf ./vcf_output/part_K03455:0..9719.vcf --min-coverage 250 --skip-coverage 0 --limit-coverage 0" +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR8525881 +K03455 2669 . 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+TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA diff -r 156b60c1530f -r ef2c525bd8cd test-data/freebayes-phix174-test1.vcf --- a/test-data/freebayes-phix174-test1.vcf Wed Oct 25 08:29:45 2017 -0400 +++ b/test-data/freebayes-phix174-test1.vcf Wed Nov 06 17:02:57 2019 -0500 @@ -1,4 +1,6 @@ ##fileformat=VCFv4.2 +##fileDate=20191030 +##source=freeBayes v1.3.1-dirty ##reference=localref.fa ##contig= ##phasing=none @@ -66,7 +68,9 @@ phiX174 1445 . C A 0.147157 . AB=0.285714;ABP=5.80219;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=7.35324;EPPR=6.91895;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=32.2;NS=1;NUMALT=1;ODDS=3.36782;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=273;RO=5;RPL=1;RPP=3.0103;RPPR=6.91895;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=2;SRP=3.44459;SRR=3;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:7:5,2:5:273:2:76:-2.52649,0,-12.4911 phiX174 1577 . A C 0.0123232 . AB=0.222222;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=7.35324;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=35.2857;NS=1;NUMALT=1;ODDS=5.8634;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=60;QR=460;RO=7;RPL=1;RPP=3.0103;RPPR=10.7656;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=3.32051;SRR=3;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:9:7,2:7:460:2:60:-1.81064,0,-19.8257 phiX174 1631 . T G 0.00100612 . AB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=4.09604;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=28;NS=1;NUMALT=1;ODDS=8.3701;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=500;RO=8;RPL=0;RPP=7.35324;RPPR=3.0103;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=4.09604;SRR=5;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:10:8,2:8:500:2:68:-1.52818,0,-17.3788 +phiX174 1665 . C A 0.0164128 . AB=0.166667;ABP=14.5915;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=2;MQM=37;MQMR=30.3333;NS=1;NUMALT=1;ODDS=5.57635;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=65;QR=587;RO=9;RPL=1;RPP=3.0103;RPPR=5.18177;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=3.25157;SRR=5;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:12:9,2:9:587:2:65:-2.35331,0,-21.269 phiX174 1772 . T G 0.0180574 . AB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=3.0103;EPPR=3.32051;GTI=0;LEN=1;MEANALT=2;MQM=31;MQMR=31.8571;NS=1;NUMALT=1;ODDS=5.48067;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=425;RO=7;RPL=1;RPP=3.0103;RPPR=3.32051;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=10.7656;SRR=6;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:10:7,2:7:425:2:59:-1.97686,0,-17.3816 +phiX174 1786 . T G 7.94817e-05 . AB=0.166667;ABP=14.5915;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=7.35324;EPPR=3.87889;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33.4;NS=1;NUMALT=1;ODDS=10.9085;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=537;RO=10;RPL=0;RPP=7.35324;RPPR=6.48466;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=16.9077;SRR=9;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:12:10,2:10:537:2:59:-0.861483,0,-25.1364 phiX174 1945 . T G 1.01422 . AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=37;NS=1;NUMALT=1;ODDS=1.3354;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=263;RO=4;RPL=1;RPP=3.0103;RPPR=5.18177;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=3.0103;SRR=2;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:6:4,2:4:263:2:59:-3.25425,0,-11.8637 phiX174 2230 . T G 0.00580188 . AB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=35.5;NS=1;NUMALT=1;ODDS=6.61746;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=80;QR=491;RO=8;RPL=0;RPP=7.35324;RPPR=4.09604;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=4.09604;SRR=5;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:10:8,2:8:491:2:80:-2.28934,0,-22.3591 phiX174 2699 . C A 2.04855 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=37;NS=1;NUMALT=1;ODDS=0.517362;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=109;RO=2;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=7.35324;SRR=2;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:4:2,2:2:109:2:76:-3.4054,0,-5.58455 @@ -76,10 +80,14 @@ phiX174 2983 . T G 1.55467 . AB=0.4;ABP=3.44459;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.0103;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=33;NS=1;NUMALT=1;ODDS=0.843116;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=57;QR=150;RO=3;RPL=1;RPP=3.0103;RPPR=3.73412;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=3.73412;SRR=1;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:5:3,2:3:150:2:57:-3.34311,0,-7.61298 phiX174 3110 . T C 1.16857 . AB=0.333333;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=3;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=3.73412;EPPR=4.45795;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=35;NS=1;NUMALT=1;ODDS=1.17522;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=94;QR=361;RO=6;RPL=0;RPP=9.52472;RPPR=3.0103;RPR=3;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=1;SRP=8.80089;SRR=5;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:9:6,3:6:361:3:94:-4.02963,0,-16.4039 phiX174 3155 . T G 5.42491 . AB=0.285714;ABP=5.80219;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=3.0103;EPPR=3.44459;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=29.8;NS=1;NUMALT=1;ODDS=0.911202;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=299;RO=5;RPL=1;RPP=3.0103;RPPR=3.44459;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=4;SRP=6.91895;SRR=1;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:7:5,2:5:299:2:75:-4.38484,0,-11.5688 +phiX174 3184 . A C 0.000128182 . AB=0.153846;ABP=16.5402;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=13;DPB=13;DPRA=0;EPP=3.0103;EPPR=3.20771;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33.7273;NS=1;NUMALT=1;ODDS=10.4306;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=738;RO=11;RPL=1;RPP=3.0103;RPPR=4.78696;RPR=1;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=8;SRP=7.94546;SRR=3;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:13:11,2:11:738:2:75:-0.695464,0,-29.8019 phiX174 3325 . A C 0.0705175 . AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=31;NS=1;NUMALT=1;ODDS=4.11232;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=58;QR=284;RO=4;RPL=2;RPP=7.35324;RPPR=3.0103;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=5.18177;SRR=1;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:6:4,2:4:284:2:58:-2.65031,0,-9.66348 +phiX174 3413 . T G 0.00284067 . AB=0.181818;ABP=12.6832;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=31.6667;NS=1;NUMALT=1;ODDS=7.33194;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=57;QR=537;RO=9;RPL=1;RPP=3.0103;RPPR=3.25157;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=8;SRP=14.8328;SRR=1;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:11:9,2:9:537:2:57:-1.59087,0,-22.4183 phiX174 3418 . A C 0.000937887 . AB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=34;NS=1;NUMALT=1;ODDS=8.44033;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=60;QR=526;RO=8;RPL=2;RPP=7.35324;RPPR=4.09604;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=5;SRP=4.09604;SRR=3;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:10:8,2:8:526:2:60:-1.49768,0,-21.0207 +phiX174 3490 . A C 0.00226584 . AB=0.181818;ABP=12.6832;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=0;EPP=7.35324;EPPR=9.04217;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=34.3333;NS=1;NUMALT=1;ODDS=7.5581;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=66;QR=543;RO=9;RPL=2;RPP=7.35324;RPPR=9.04217;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=9;SRP=22.5536;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:11:9,2:9:543:2:66:-2.09471,0,-24.3433 phiX174 3729 . C T 0.295112 . AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=37;NS=1;NUMALT=1;ODDS=2.65478;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=63;QR=232;RO=4;RPL=2;RPP=7.35324;RPPR=5.18177;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=11.6962;SRR=4;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:6:4,2:4:232:2:63:-3.28331,0,-11.7007 phiX174 4031 . T G 0.0784807 . AB=0.25;ABP=7.35324;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=7.35324;EPPR=4.45795;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=27;NS=1;NUMALT=1;ODDS=4.00441;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=85;QR=322;RO=6;RPL=2;RPP=7.35324;RPPR=8.80089;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=3.0103;SRR=3;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:8:6,2:6:322:2:85:-3.02817,0,-11.6802 phiX174 4502 . A C 0.232919 . AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=37;NS=1;NUMALT=1;ODDS=2.89868;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=55;QR=284;RO=4;RPL=1;RPP=3.0103;RPPR=11.6962;RPR=1;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=5.18177;SRR=1;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:6:4,2:4:284:2:55:-2.57533,0,-11.8832 phiX174 4558 . C G 0.076247 . AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=28;NS=1;NUMALT=1;ODDS=4.03372;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=204;RO=4;RPL=2;RPP=7.35324;RPPR=11.6962;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=2;SRP=3.0103;SRR=2;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:6:4,2:4:204:2:59:-2.68445,0,-8.4362 phiX174 4655 . T G 0.399408 . AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=37;NS=1;NUMALT=1;ODDS=2.33999;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=193;RO=4;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=0;SRP=11.6962;SRR=4;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:6:4,2:4:193:2:70:-2.81796,0,-11.1489 +phiX174 4704 . T C 0.000171782 . AB=0.166667;ABP=14.5915;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=7.35324;EPPR=10.8276;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=33.4;NS=1;NUMALT=1;ODDS=10.1378;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=58;QR=621;RO=10;RPL=0;RPP=7.35324;RPPR=3.87889;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=4;SRP=3.87889;SRR=6;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0/1:12:10,2:10:621:2:58:-1.1962,0,-26.2058 diff -r 156b60c1530f -r ef2c525bd8cd test-data/freebayes-phix174-test2.vcf --- a/test-data/freebayes-phix174-test2.vcf Wed Oct 25 08:29:45 2017 -0400 +++ b/test-data/freebayes-phix174-test2.vcf Wed Nov 06 17:02:57 2019 -0500 @@ -1,8 +1,10 @@ ##fileformat=VCFv4.2 +##fileDate=20191031 +##source=freeBayes v1.3.1-dirty ##reference=localref.fa ##contig= ##phasing=none -##commandline="freebayes --region phiX174:0..5386 --bam b_0.bam --fasta-reference localref.fa --vcf ./vcf_output/part_phiX174:0..5386.vcf --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0 --pooled-continuous --report-monomorphic --standard-filters --min-coverage 14" +##commandline="freebayes --region phiX174:0..5386 --bam b_0.bam --fasta-reference localref.fa --vcf ./vcf_output/part_phiX174:0..5386.vcf --min-coverage 14 --skip-coverage 0 --limit-coverage 0 --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0.05 --pooled-continuous --report-monomorphic --standard-filters" ##INFO= ##INFO= ##INFO= diff -r 156b60c1530f -r ef2c525bd8cd test-data/freebayes-phix174-test3.vcf --- a/test-data/freebayes-phix174-test3.vcf Wed Oct 25 08:29:45 2017 -0400 +++ b/test-data/freebayes-phix174-test3.vcf Wed Nov 06 17:02:57 2019 -0500 @@ -1,8 +1,10 @@ ##fileformat=VCFv4.2 +##fileDate=20191031 +##source=freeBayes v1.3.1-dirty ##reference=localref.fa ##contig= ##phasing=none -##commandline="freebayes --region phiX174:0..5386 --bam b_0.bam --fasta-reference localref.fa --vcf ./vcf_output/part_phiX174:0..5386.vcf --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0 --pooled-continuous --report-monomorphic --standard-filters --min-coverage 14" +##commandline="freebayes --region phiX174:0..5386 --bam b_0.bam --fasta-reference localref.fa --vcf ./vcf_output/part_phiX174:0..5386.vcf --min-coverage 14 --skip-coverage 0 --limit-coverage 0 --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0.05 --pooled-continuous --report-monomorphic --standard-filters" ##INFO= ##INFO= ##INFO= diff -r 156b60c1530f -r ef2c525bd8cd test-data/freebayes-phix174-test4.vcf --- a/test-data/freebayes-phix174-test4.vcf Wed Oct 25 08:29:45 2017 -0400 +++ b/test-data/freebayes-phix174-test4.vcf Wed Nov 06 17:02:57 2019 -0500 @@ -1,4 +1,6 @@ ##fileformat=VCFv4.2 +##fileDate=20191030 +##source=freeBayes v1.3.1-dirty ##reference=localref.fa ##contig= ##phasing=none @@ -66,7 +68,9 @@ phiX174 1445 . C A 3.85961e-09 . AB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=7.35324;EPPR=6.91895;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=32.2;NS=1;NUMALT=1;ODDS=20.8413;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=273;RO=5;RPL=1;RPP=3.0103;RPPR=6.91895;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=2;SRP=3.44459;SRR=3;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0:7:5,2:5:273:2:76:0,-9.96463 phiX174 1577 . A C 7.60962e-15 . AB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=7.35324;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=35.2857;NS=1;NUMALT=1;ODDS=38.7543;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=60;QR=460;RO=7;RPL=1;RPP=3.0103;RPPR=10.7656;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=3.32051;SRR=3;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0:9:7,2:7:460:2:60:0,-18.0151 phiX174 1631 . T G 8.14828e-15 . AB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=4.09604;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=28;NS=1;NUMALT=1;ODDS=36.3199;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=500;RO=8;RPL=0;RPP=7.35324;RPPR=3.0103;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=4.09604;SRR=5;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0:10:8,2:8:500:2:68:0,-15.8506 +phiX174 1665 . C A 1.45784e-14 . AB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=2;MQM=37;MQMR=30.3333;NS=1;NUMALT=1;ODDS=41.3105;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=65;QR=587;RO=9;RPL=1;RPP=3.0103;RPPR=5.18177;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=3.25157;SRR=5;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0:12:9,2:9:587:2:65:0,-18.9157 phiX174 1772 . T G 2.89903e-14 . AB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=3.0103;EPPR=3.32051;GTI=0;LEN=1;MEANALT=2;MQM=31;MQMR=31.8571;NS=1;NUMALT=1;ODDS=32.7439;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=425;RO=7;RPL=1;RPP=3.0103;RPPR=3.32051;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=10.7656;SRR=6;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0:10:7,2:7:425:2:59:0,-15.4048 +phiX174 1786 . T G 0 . AB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=7.35324;EPPR=3.87889;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33.4;NS=1;NUMALT=1;ODDS=51.6968;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=537;RO=10;RPL=0;RPP=7.35324;RPPR=6.48466;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=16.9077;SRR=9;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0:12:10,2:10:537:2:59:0,-24.2749 phiX174 1945 . T G 2.84647e-08 . AB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=37;NS=1;NUMALT=1;ODDS=18.8432;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=263;RO=4;RPL=1;RPP=3.0103;RPPR=5.18177;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=3.0103;SRR=2;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0:6:4,2:4:263:2:59:0,-8.60945 phiX174 2230 . T G 1.46203e-15 . AB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=35.5;NS=1;NUMALT=1;ODDS=46.0348;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=80;QR=491;RO=8;RPL=0;RPP=7.35324;RPPR=4.09604;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=4.09604;SRR=5;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0:10:8,2:8:491:2:80:0,-20.0697 phiX174 2699 . C A 0.0286554 . AB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=37;NS=1;NUMALT=1;ODDS=5.01766;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=109;RO=2;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=7.35324;SRR=2;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0:4:2,2:2:109:2:76:0,-2.17914 @@ -76,10 +80,14 @@ phiX174 2983 . T G 0.000276493 . AB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.0103;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=33;NS=1;NUMALT=1;ODDS=9.66185;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=57;QR=150;RO=3;RPL=1;RPP=3.0103;RPPR=3.73412;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=3.73412;SRR=1;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0:5:3,2:3:150:2:57:0,-4.26987 phiX174 3110 . T C 4.70002e-12 . AB=0;ABP=0;AC=0;AF=0;AN=1;AO=3;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=3.73412;EPPR=4.45795;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=35;NS=1;NUMALT=1;ODDS=27.5529;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=94;QR=361;RO=6;RPL=0;RPP=9.52472;RPPR=3.0103;RPR=3;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=1;SRP=8.80089;SRR=5;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0:9:6,3:6:361:3:94:0,-12.3743 phiX174 3155 . T G 1.16474e-06 . AB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=3.0103;EPPR=3.44459;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=29.8;NS=1;NUMALT=1;ODDS=15.1316;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=299;RO=5;RPL=1;RPP=3.0103;RPPR=3.44459;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=4;SRP=6.91895;SRR=1;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0:7:5,2:5:299:2:75:0,-7.18392 +phiX174 3184 . A C 0 . AB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=13;DPB=13;DPRA=0;EPP=3.0103;EPPR=3.20771;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33.7273;NS=1;NUMALT=1;ODDS=63.9593;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=738;RO=11;RPL=1;RPP=3.0103;RPPR=4.78696;RPR=1;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=8;SRP=7.94546;SRR=3;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0:13:11,2:11:738:2:75:0,-29.1064 phiX174 3325 . A C 2.80881e-07 . AB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=31;NS=1;NUMALT=1;ODDS=16.5539;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=58;QR=284;RO=4;RPL=2;RPP=7.35324;RPPR=3.0103;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=5.18177;SRR=1;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0:6:4,2:4:284:2:58:0,-7.01317 +phiX174 3413 . T G 6.16289e-15 . AB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=31.6667;NS=1;NUMALT=1;ODDS=43.4788;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=57;QR=537;RO=9;RPL=1;RPP=3.0103;RPPR=3.25157;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=8;SRP=14.8328;SRR=1;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0:11:9,2:9:537:2:57:0,-20.8274 phiX174 3418 . A C 0 . AB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=34;NS=1;NUMALT=1;ODDS=44.7759;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=60;QR=526;RO=8;RPL=2;RPP=7.35324;RPPR=4.09604;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=5;SRP=4.09604;SRR=3;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0:10:8,2:8:526:2:60:0,-19.523 +phiX174 3490 . A C 0 . AB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=0;EPP=7.35324;EPPR=9.04217;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=34.3333;NS=1;NUMALT=1;ODDS=43.8402;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=66;QR=543;RO=9;RPL=2;RPP=7.35324;RPPR=9.04217;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=9;SRP=22.5536;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0:11:9,2:9:543:2:66:0,-22.2486 phiX174 3729 . C T 6.64464e-08 . AB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=37;NS=1;NUMALT=1;ODDS=17.9954;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=63;QR=232;RO=4;RPL=2;RPP=7.35324;RPPR=5.18177;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=11.6962;SRR=4;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0:6:4,2:4:232:2:63:0,-8.41737 phiX174 4031 . T G 2.20192e-08 . AB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=7.35324;EPPR=4.45795;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=27;NS=1;NUMALT=1;ODDS=19.0999;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=85;QR=322;RO=6;RPL=2;RPP=7.35324;RPPR=8.80089;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=3.0103;SRR=3;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0:8:6,2:6:322:2:85:0,-8.65207 phiX174 4502 . A C 3.4202e-08 . AB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=37;NS=1;NUMALT=1;ODDS=18.6595;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=55;QR=284;RO=4;RPL=1;RPP=3.0103;RPPR=11.6962;RPR=1;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=5.18177;SRR=1;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0:6:4,2:4:284:2:55:0,-9.30785 phiX174 4558 . C G 1.36745e-05 . AB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=28;NS=1;NUMALT=1;ODDS=12.6685;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=204;RO=4;RPL=2;RPP=7.35324;RPPR=11.6962;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=2;SRP=3.0103;SRR=2;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0:6:4,2:4:204:2:59:0,-5.75175 phiX174 4655 . T G 1.44134e-07 . AB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=37;NS=1;NUMALT=1;ODDS=17.2211;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=193;RO=4;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=0;SRP=11.6962;SRR=4;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0:6:4,2:4:193:2:70:0,-8.33095 +phiX174 4704 . T C 1.08534e-15 . AB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=7.35324;EPPR=10.8276;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=33.4;NS=1;NUMALT=1;ODDS=55.4522;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=58;QR=621;RO=10;RPL=0;RPP=7.35324;RPPR=3.87889;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=4;SRP=3.87889;SRR=6;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0:12:10,2:10:621:2:58:0,-25.0096