5.1 allelicDepth
Writing genotype likelihoods to a GLF file
allelicDepth creates a table summarizing the composition of the bases covering each site. It is basically a flattened 4-dimensional table.
5.1.1 Input
Required inputs :
--bam Input_bam_file.bam |
Input BAM file. |
Optional inputs :
--recal recal.txt |
Quality score recalibration file (see recal for further information). |
--pmd Input_PMD.txt |
Post-mortem damage parameters (see PMD for generating such a file). |
Specific Parameters :
--readUpToDepth integer_value |
To set read depth up-to which reads are to be considered and ignore additional bases. Default = 1000. |
--filterDepth integer_value1,integer_value2 |
To filter out sites with sequencing depth outside the range [integer_value1,integer_value2]. Default = Will keep sites regardless of depth. |
--filterCpG |
To filter out CpG sites. Default = Will keep CpG sites. |
--maxRefN numeric_value |
To specify the max fraction of sites with reference=‘N’ in a window, for the window to still be considered. numeric_value must be between 0 and 1 (inclusive). Default = 1. |
--filterBaseQual integer_value1,integer_value2 |
To filter out bases with quality outside the range [integer_value1,integer_value2]. Default = [1,93]. |
--ignoreContexts |
To filter out bases based on context. Default = keep bases regardless of base context. |
--printAll |
To print cells with zero counts as well. Default = Will only print cells with non-zero counts. |
Engine parameters that are common to all tasks can be found here.