U2::LocalWorkflow::CallVariantsPrompter unset unset For reference sequence from <u>%1</u>, For reference sequence from <u>%1</u>, with assembly data provided by <u>%1</u> with assembly data provided by <u>%1</u> %1 call variants %2. %1 call variants %2. U2::LocalWorkflow::CallVariantsTask Call variants for %1 Call variants for %1 reference reference assembly assembly The %1 file does not exist: %2 The %1 file does not exist: %2 No assembly files No assembly files No dbi storage No dbi storage No sequence URL No sequence URL No document loaded No document loaded Incorrect variant track object in %1 Incorrect variant track object in %1 U2::LocalWorkflow::CallVariantsWorker Empty input slot: %1 Empty input slot: %1 Input sequences Input sequences A nucleotide reference sequence. A nucleotide reference sequence. Input assembly Input assembly Position sorted alignment file Position sorted alignment file Output variations Output variations Output tracks with SNPs and short INDELs Output tracks with SNPs and short INDELs Call Variants with SAMtools Call Variants with SAMtools Calls SNPs and INDELS with SAMtools mpileup and bcftools. Calls SNPs and INDELS with SAMtools mpileup and bcftools. Output variants file Output variants file The url to the file with the extracted variations. The url to the file with the extracted variations. Use reference from <p>Specify "File" to set a single reference sequence for all input NGS assemblies. The reference should be set in the "Reference" parameter.</p><p>Specify "Input port" to be able to set different references for difference NGS assemblies. The references should be input via the "Input sequences" port (e.g. use datasets in the "Read Sequence" element).</p> Reference <p>Specify a file with the reference sequence.</p><p>The sequence will be used as reference for all datasets with NGS assemblies.</p> Illumina-1.3+ encoding Illumina-1.3+ encoding Assume the quality is in the Illumina 1.3+ encoding (mpileup)(-6). Assume the quality is in the Illumina 1.3+ encoding (mpileup)(-6). Count anomalous read pairs Count anomalous read pairs Do not skip anomalous read pairs in variant calling(mpileup)(-A). Do not skip anomalous read pairs in variant calling(mpileup)(-A). Disable BAQ computation Disable BAQ computation Disable probabilistic realignment for the computation of base alignment quality (BAQ). BAQ is the Phred-scaled probability of a read base being misaligned. Applying this option greatly helps to reduce false SNPs caused by misalignments. (mpileup)(-B). Disable probabilistic realignment for the computation of base alignment quality (BAQ). BAQ is the Phred-scaled probability of a read base being misaligned. Applying this option greatly helps to reduce false SNPs caused by misalignments. (mpileup)(-B). Mapping quality downgrading coefficient Mapping quality downgrading coefficient Coefficient for downgrading mapping quality for reads containing excessive mismatches. Given a read with a phred-scaled mapping quality q of being generated from the mapped position, the new mapping quality is about sqrt((INT-q)/INT)*INT. A zero value disables this functionality; if enabled, the recommended value for BWA is 50 (mpileup)(-C). Coefficient for downgrading mapping quality for reads containing excessive mismatches. Given a read with a phred-scaled mapping quality q of being generated from the mapped position, the new mapping quality is about sqrt((INT-q)/INT)*INT. A zero value disables this functionality; if enabled, the recommended value for BWA is 50 (mpileup)(-C). Max number of reads per input BAM Max number of reads per input BAM At a position, read maximally the number of reads per input BAM (mpileup)(-d). At a position, read maximally the number of reads per input BAM (mpileup)(-d). Extended BAQ computation Extended BAQ computation Extended BAQ computation. This option helps sensitivity especially for MNPs, but may hurt specificity a little bit (mpileup)(-E). Extended BAQ computation. This option helps sensitivity especially for MNPs, but may hurt specificity a little bit (mpileup)(-E). BED or position list file BED or position list file BED or position list file containing a list of regions or sites where pileup or BCF should be generated (mpileup)(-l). BED or position list file containing a list of regions or sites where pileup or BCF should be generated (mpileup)(-l). Pileup region Pileup region Only generate pileup in region STR (mpileup)(-r). Only generate pileup in region STR (mpileup)(-r). Minimum mapping quality Minimum mapping quality Minimum mapping quality for an alignment to be used (mpileup)(-q). Minimum mapping quality for an alignment to be used (mpileup)(-q). Minimum base quality Minimum base quality Minimum base quality for a base to be considered (mpileup)(-Q). Minimum base quality for a base to be considered (mpileup)(-Q). Gap extension error Gap extension error Phred-scaled gap extension sequencing error probability. Reducing INT leads to longer indels (mpileup)(-e). Phred-scaled gap extension sequencing error probability. Reducing INT leads to longer indels (mpileup)(-e). Homopolymer errors coefficient Homopolymer errors coefficient Coefficient for modeling homopolymer errors. Given an l-long homopolymer run, the sequencing error of an indel of size s is modeled as INT*s/l (mpileup)(-h). Coefficient for modeling homopolymer errors. Given an l-long homopolymer run, the sequencing error of an indel of size s is modeled as INT*s/l (mpileup)(-h). No INDELs No INDELs Do not perform INDEL calling (mpileup)(-I). Do not perform INDEL calling (mpileup)(-I). Max INDEL depth Max INDEL depth Skip INDEL calling if the average per-sample depth is above INT (mpileup)(-L). Skip INDEL calling if the average per-sample depth is above INT (mpileup)(-L). Gap open error Gap open error Phred-scaled gap open sequencing error probability. Reducing INT leads to more indel calls (mpileup)(-o). Phred-scaled gap open sequencing error probability. Reducing INT leads to more indel calls (mpileup)(-o). List of platforms for indels List of platforms for indels Comma dilimited list of platforms (determined by @RG-PL) from which indel candidates are obtained.It is recommended to collect indel candidates from sequencing technologies that have low indel error rate such as ILLUMINA (mpileup)(-P). Comma dilimited list of platforms (determined by @RG-PL) from which indel candidates are obtained.It is recommended to collect indel candidates from sequencing technologies that have low indel error rate such as ILLUMINA (mpileup)(-P). Retain all possible alternate Retain all possible alternate Retain all possible alternate alleles at variant sites. By default, the view command discards unlikely alleles (bcf view)(-A). Retain all possible alternate alleles at variant sites. By default, the view command discards unlikely alleles (bcf view)(-A). Indicate PL Indicate PL Indicate PL is generated by r921 or before (ordering is different) (bcf view)(-F). Indicate PL is generated by r921 or before (ordering is different) (bcf view)(-F). No genotype information No genotype information Suppress all individual genotype information (bcf view)(-G). Suppress all individual genotype information (bcf view)(-G). A/C/G/T only A/C/G/T only Skip sites where the REF field is not A/C/G/T (bcf view)(-N). Skip sites where the REF field is not A/C/G/T (bcf view)(-N). List of sites List of sites List of sites at which information are outputted (bcf view)(-l). List of sites at which information are outputted (bcf view)(-l). QCALL likelihood QCALL likelihood Output the QCALL likelihood format (bcf view)(-Q). Output the QCALL likelihood format (bcf view)(-Q). List of samples List of samples List of samples to use. The first column in the input gives the sample names and the second gives the ploidy, which can only be 1 or 2. When the 2nd column is absent, the sample ploidy is assumed to be 2. In the output, the ordering of samples will be identical to the one in FILE (bcf view)(-s). List of samples to use. The first column in the input gives the sample names and the second gives the ploidy, which can only be 1 or 2. When the 2nd column is absent, the sample ploidy is assumed to be 2. In the output, the ordering of samples will be identical to the one in FILE (bcf view)(-s). Min samples fraction Min samples fraction skip loci where the fraction of samples covered by reads is below FLOAT (bcf view)(-d). skip loci where the fraction of samples covered by reads is below FLOAT (bcf view)(-d). Per-sample genotypes Per-sample genotypes Call per-sample genotypes at variant sites (bcf view)(-g). Call per-sample genotypes at variant sites (bcf view)(-g). INDEL-to-SNP Ratio INDEL-to-SNP Ratio Ratio of INDEL-to-SNP mutation rate (bcf view)(-i). Ratio of INDEL-to-SNP mutation rate (bcf view)(-i). Max P(ref|D) Max P(ref|D) A site is considered to be a variant if P(ref|D)<FLOAT (bcf view)(-p). A site is considered to be a variant if P(ref|D) less than FLOAT (bcf view)(-p). Prior allele frequency spectrum Prior allele frequency spectrum If STR can be full, cond2, flat or the file consisting of error output from a previous variant calling run (bcf view)(-P). If STR can be full, cond2, flat or the file consisting of error output from a previous variant calling run (bcf view)(-P). Mutation rate Mutation rate Scaled mutation rate for variant calling (bcf view)(-t). Scaled mutation rate for variant calling (bcf view)(-t). Pair/trio calling Pair/trio calling Enable pair/trio calling. For trio calling, option -s is usually needed to be applied to configure the trio members and their ordering. In the file supplied to the option -s, the first sample must be the child, the second the father and the third the mother. The valid values of STR are '‘pair’', '‘trioauto’', '‘trioxd’' and '‘trioxs’', where '‘pair’' calls differences between two input samples, and '‘trioxd’' ('‘trioxs’')specifies that the input is from the X chromosome non-PAR regions and the child is a female (male) (bcf view)(-T). Enable pair/trio calling. For trio calling, option -s is usually needed to be applied to configure the trio members and their ordering. In the file supplied to the option -s, the first sample must be the child, the second the father and the third the mother. The valid values of STR are '‘pair’', '‘trioauto’', '‘trioxd’' and '‘trioxs’', where '‘pair’' calls differences between two input samples, and '‘trioxd’' ('‘trioxs’')specifies that the input is from the X chromosome non-PAR regions and the child is a female (male) (bcf view)(-T). Enable pair/trio calling. For trio calling, option -s is usually needed to be applied to configure the trio members and their ordering. In the file supplied to the option -s, the first sample must be the child, the second the father and the third the mother. The valid values of STR are '‘pair’', '‘trioauto’', '‘trioxd’' and '‘trioxs’', where '‘pair’' calls differences between two input samples, and '‘trioxd’' ('‘trioxs’')specifies that the input is from the X chromosome non-PAR regions and the child is a female (male) (bcf view)(-T). N group-1 samples N group-1 samples Number of group-1 samples. This option is used for dividing the samples into two groups for contrast SNP calling or association test. When this option is in use, the followingVCF INFO will be outputted: PC2, PCHI2 and QCHI2 (bcf view)(-1). Number of group-1 samples. This option is used for dividing the samples into two groups for contrast SNP calling or association test. When this option is in use, the followingVCF INFO will be outputted: PC2, PCHI2 and QCHI2 (bcf view)(-1). N permutations N permutations Number of permutations for association test (effective only with -1) (bcf view)(-U). Number of permutations for association test (effective only with -1) (bcf view)(-U). Max P(chi^2) Max P(chi^2) Only perform permutations for P(chi^2)<FLOAT (N permutations) (bcf view)(-X). Only perform permutations for P(chi^2)<FLOAT (N permutations) (bcf view)(-X). Minimum RMS quality Minimum RMS quality Minimum RMS mapping quality for SNPs (varFilter) (-Q). Minimum RMS mapping quality for SNPs (varFilter) (-Q). Minimum read depth Minimum read depth Minimum read depth (varFilter) (-d). Minimum read depth (varFilter) (-d). Maximum read depth Maximum read depth Maximum read depth (varFilter) (-D). Maximum read depth (varFilter) (-D). Alternate bases Alternate bases Minimum number of alternate bases (varFilter) (-a). Minimum number of alternate bases (varFilter) (-a). Gap size Gap size SNP within INT bp around a gap to be filtered (varFilter) (-w). SNP within INT bp around a gap to be filtered (varFilter) (-w). Window size Window size Window size for filtering adjacent gaps (varFilter) (-W). Window size for filtering adjacent gaps (varFilter) (-W). Strand bias Strand bias Minimum P-value for strand bias (given PV4) (varFilter) (-1). Minimum P-value for strand bias (given PV4) (varFilter) (-1). BaseQ bias BaseQ bias Minimum P-value for baseQ bias (varFilter) (-2). Minimum P-value for baseQ bias (varFilter) (-2). MapQ bias MapQ bias Minimum P-value for mapQ bias (varFilter) (-3). Minimum P-value for mapQ bias (varFilter) (-3). End distance bias End distance bias Minimum P-value for end distance bias (varFilter) (-4). Minimum P-value for end distance bias (varFilter) (-4). HWE HWE Minimum P-value for HWE (plus F<0) (varFilter) (-e). Minimum P-value for HWE (plus F<0) (varFilter) (-e). Log filtered Log filtered Print filtered variants into the log (varFilter) (-p). Print filtered variants into the log (varFilter) (-p). Input port File Assembly URL slot is empty. Please, specify the URL slot Assembly URL slot is empty. Please, specify the URL slot Ref sequence URL slot is empty. Please, specify the URL slot Ref sequence URL slot is empty. Please, specify the URL slot Not enough references Not enough references The dataset slot is not binded, only the first reference sequence against all assemblies was processed. The dataset slot is not binded, only the first reference sequence against all assemblies was processed. Not enough assemblies Not enough assemblies U2::LocalWorkflow::SamtoolsMpileupTask Samtool mpileup for %1 Samtool mpileup for %1 No reference sequence URL to do pileup No reference sequence URL to do pileup No assembly URL to do pileup No assembly URL to do pileup There is an assembly with an empty path There is an assembly with an empty path Can not create the folder: Can not create the folder: Can not run %1 tool Can not run %1 tool %1 tool exited with code %2 %1 tool exited with code %2 Tool %1 finished successfully Tool %1 finished successfully U2::SamtoolsPlugin Samtools plugin Samtools plugin Samtools plugin for NGS data analysis Samtools plugin for NGS data analysis