--limitLines numLines |
Limit amount of lines to be read from VCF file. |
all lines |
--filterDepth min,max |
Keep only the samples with indicated sample depth (inclusive). |
keep all |
--maxMissing fraction |
Filter out sites which has more than the indicated data fraction missing. numeric_value must be between 0 and 1 (inclusive). |
keep all |
--minMAF MAFmin |
only store sites where initial estimate of allele frequency is larger or equal to minMAF. |
0.0 |
--minVarQual QualMin |
Only store sites with minimum variant quality as indicated or more. |
keep all |