Variants Calling

Task Name: snp

Call variants for an input assembly and a reference sequence using SAMtools mpileup and bcftools.

Parameters:

bam - Input sorted BAM file(s) [URL datasets]
ref - Input reference sequence [URL datasets]
wout - Output file with variations [String]
bN - A/C/G/T only [Boolean]
bI - List of sites [String]
ml - BED or position list file [String]
bg - Per-sample genotypes [Boolean]
mC - Mapping quality downgrading coefficient [Number]
bT - Pair/trio calling [String]
mB - Disable BAQ computation [Boolean]
me - Gap extension error [Number]
mE - Extended BAQ computation [Boolean]
bF - Indicate PL [Boolean]
vw - Gap size [Number]
m6 - Illumina-1.3+ encoding [Boolean]
bi - INDEL-to-SNP Ratio [Number]
bA - Retain all possible alternates [Boolean]
vD - Max number of reads per input BAM [Number]
md - Max number of reads per input BAM [Number]
mL - Max INDEL depth [Number]
va - Alternate bases [Number]
v2 - BaseQ bias [String]
vd - Minimum read depth [Number]
v4 - End distance bias [Number]
v3 - MapQ bias [Number]
Q - Minimum RMS quality [Number]
v1 - Strand bias [Number]
mQ - Minimum base quality [Number]
mq - Minimum mapping quality [Number]
bd - Min samples fraction [Number]
b1 - N group-1 samples [Number]
bU - N permutations [Number]
bG - No genotype information [Boolean]
mI - No INDELs [Boolean]
mo - Gap open error [Number]
mP - List of platforms for indels [String]
vp - Log filtered [Boolean]
bP - Prior allele frequency spectrum [String]
bQ - QCALL likelihood [Boolean]
mr - Pileup region [String]
bs - List of samples [String]
mh - Homopolymer errors coefficient [Number]
bt - Mutation rate [Number]
mA - Count anomalous read pairs [Boolean]
vW - A/C/G/T only [Number]

Example:

ugene snp --bam=test.bam --ref=test_ref.fa --wout=test_out.vcf