Alignment coverage information maf_stats.py #if $maf_source_type.maf_source == "user": $maf_source_type.maf_source $input2 $input1 $out_file1 $dbkey ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} $summary #else: $maf_source_type.maf_source $maf_source_type.mafType $input1 $out_file1 $dbkey ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} $summary #end if ${GALAXY_DATA_INDEX_DIR} #if $maf_source_type.maf_source == "user": $input2.metadata.maf_index #end if Locally Cached Alignments Alignments in Your History Coverage by Region Summarize Coverage numpy

**What it does** This tool takes a MAF file and an interval file and relates coverage information by interval for each species. If a column does not exist in the reference genome, it is not included in the output. Consider the interval: "chrX 1000 1100 myInterval" Let's suppose we want to do stats on three way alignments for H, M, and R. The result look like this: chrX 1000 1100 myInterval H XXX YYY chrX 1000 1100 myInterval M XXX YYY chrX 1000 1100 myInterval R XXX YYY where XXX and YYY are: XXX = number of nucleotides YYY = number of gaps ---- Alternatively, you can request only summary information for a set of intervals: ======== =========== ======== #species nucleotides coverage ======== =========== ======== hg18 30639 0.2372 rheMac2 7524 0.0582 panTro2 30390 0.2353 ======== =========== ======== where **coverage** is the number of nucleotides divided by the total length of the provided intervals.