Call Variants with SAMtools Element

Calls SNPs and INDELS with SAMtools mpileup and bcftools.

Element type: call_variants

Parameters

Parameter	Description	Default value	Parameter in Workflow File	Type
Output variants file	The URL to the file with the extracted variations.
Reference	File with the reference sequence for all NGS assemblies.			string
Use reference from	`File` (use same reference for all inputs) or `Input port` (different references via input port).	File		string
Illumina-1.3+ encoding	Assume Illumina 1.3+ quality encoding (mpileup `-6`).	False	illumina13-encoding	boolean
Count anomalous read pairs	Do not skip anomalous read pairs (mpileup `-A`).	False	use_orphan	boolean
Disable BAQ computation	Disable base alignment quality calculation (mpileup `-B`).	False	disable_baq	boolean
Mapping quality downgrade	Downgrade mapping quality for mismatched reads (mpileup `-C`). Recommended for BWA: 50.	0	capq_thres	numeric
Max reads per BAM	Limit number of reads per position (mpileup `-d`).	250	max_depth	numeric
Extended BAQ computation	Improves MNP sensitivity (mpileup `-E`).	False	ext_baq	boolean
BED or position list file	Regions to generate pileup for (mpileup `-l`).		bed	string
Pileup region	Region to generate pileup (mpileup `-r`).		reg	string
Minimum mapping quality	Minimum mapping quality for alignments (mpileup `-q`).	0	min_mq	numeric
Minimum base quality	Minimum base quality (mpileup `-Q`).	13	min_baseq	numeric
Gap extension error	Error probability for gap extension (mpileup `-e`).	20	extQ	numeric
Homopolymer error coefficient	Error model coefficient for indels in homopolymers (mpileup `-h`).	100	tandemQ	numeric
No INDELs	Do not call INDELs (mpileup `-I`).	False	no_indel	boolean
Max INDEL depth	Skip INDELs above per-sample depth (mpileup `-L`).	250	max_indel_depth	numeric
Gap open error	Gap open error probability (mpileup `-o`).	40	openQ	numeric
Platform list for indels	Comma-separated list of platforms for indels (mpileup `-P`).		pl_list	string
Retain all alternates	Keep all alternate alleles (bcftools view `-A`).	False	keepalt	boolean
Indicate PL	PL from older SAMtools versions (bcftools view `-F`).	False	fix_pl	boolean
No genotype information	Suppress genotypes (bcftools view `-G`).	False	no_geno	boolean
A/C/G/T only	Skip sites where REF is not A/C/G/T (bcftools view `-N`).	False	acgt_only	boolean
List of sites	Limit to listed sites (bcftools view `-l`).		bcf_bed	string
QCALL likelihood	Output QCALL format (bcftools view `-Q`).	False	qcall	boolean
Sample list	File with sample names and ploidy (bcftools view `-s`).		samples	string
Min sample fraction	Skip loci if < fraction of samples are covered (bcftools view `-d`).	0	min_smpl_frac	numeric
Per-sample genotypes	Call genotypes (bcftools view `-g`).	True	call_gt	boolean
INDEL-to-SNP ratio	Expected mutation ratio (bcftools view `-i`).	-1	indel_frac	numeric
**Max P(ref	D)**	Site considered variant if probability of reference is below (bcftools view).	0.5	pref
Allele frequency prior	Allele frequency prior: `full`, `cond2`, `flat`, or previous run output (bcftools view `-P`).	full	ptype	string
Mutation rate	Mutation rate (bcftools view `-t`).	0.001	theta	numeric
Pair/trio calling	Enable pair/trio calling (bcftools view `-T`).		ccall	string
N group-1 samples	Number of group-1 samples for association test (bcftools view `-1`).	0	n1	numeric
N permutations	Permutations for association test (bcftools view `-U`).	0	n_perm	numeric
Min P(chi²)	Threshold for P(chi²) to perform permutations.	0.01	min_perm_p	numeric
Min RMS quality	Minimum RMS mapping quality for SNPs (varFilter `-Q`).	10	min-qual	numeric
Min read depth	Minimum read depth (varFilter `-d`).	2	min-dep	numeric
Max read depth	Maximum read depth (varFilter `-D`).	10000000	max-dep	numeric
Alternate bases	Minimum alternate base count (varFilter `-a`).	2	min-alt-bases	numeric
Gap size	SNPs within this distance of a gap are filtered (varFilter `-w`).	3	gap-size	numeric
Window size	Filtering window for adjacent gaps (varFilter `-W`).	10	window	numeric
Strand bias	P-value threshold for strand bias (varFilter `-1`).	0.0001	min-strand	numeric
BaseQ bias	Minimum P-value for baseQ bias (varFilter `-2`).	1e-100	min-baseQ	string
MapQ bias	Minimum P-value for mapping quality bias (varFilter `-3`).	0	min-mapQ	numeric
End distance bias	Minimum P-value for bias near sequence ends (varFilter `-4`).	0.0001	min-end-distance	numeric
HWE	Minimum P-value for Hardy-Weinberg Equilibrium + F<0 (varFilter `-e`).	0.0001	min-hwe	numeric
Log filtered	Print filtered variants to log (varFilter `-p`).	False	print-filtered	boolean

Input/Output Ports

The element has 2 input ports:

Name in GUI: Input assembly
Name in Workflow File: in-assembly

Slot In GUI	Slot in Workflow File	Type
Dataset name	dataset	string
Source url	url	string

Name in GUI: Input sequences
Name in Workflow File: in-sequence

Slot In GUI	Slot in Workflow File	Type
Source url	url	string

And 1 output port:

Name in GUI: Output variations
Name in Workflow File: out-variations

Slot In GUI	Slot in Workflow File	Type
Variation track	variation-track	variation