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1,235 bytes added
, 10:26, 29 September 2011
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| *TotalBases - # of bases in all reads | | *TotalBases - # of bases in all reads |
| *BasesInMappedReads - # of bases in reads marked mapped in the flag | | *BasesInMappedReads - # of bases in reads marked mapped in the flag |
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| == Qual/Phred == | | == Qual/Phred == |
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| *AverageMapQualCount - # of mapping qualities used to calculate AverageMapQuality. | | *AverageMapQualCount - # of mapping qualities used to calculate AverageMapQuality. |
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| + | Currently there is no special logic to exclude positions where the refernce is 'N'. |
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| + | Currently there is no special logic to exclude reads from the counts when the base is 'N'. |
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− | Currently there is no special logic to exclude positions where the refernce is 'N'.
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− | Currently there is no special logic to exclude reads from the counts when the base is 'N'.
| + | === Output Format ==== |
| + | Order: |
| + | *chrom - Chromosome/reference name string from the SAM/BAM |
| + | *chromStart - 0-based start position |
| + | *chromEnd - 0-based end position (always 1 greater than start and not included in this region) |
| + | *Depth - excludes unmapped reads, duplicates, failed QC, deletions/skips (only CIGAR M/X/= are included), MapQ below the min |
| + | *Q20Bases - excludes unmapped reads, duplicates, failed QC, deletions/skips (only CIGAR M/X/= are included), MapQ below the min |
| + | *Q20BasesPct(%) - excludes unmapped reads, duplicates, failed QC, deletions/skips (only CIGAR M/X/= are included), MapQ below the min |
| + | *TotalReads - only excludes clips |
| + | *MappedBases - only excludes clips |
| + | *MappingRate(%) - only excludes clips |
| + | *MapRate_MQPass(%) - only excludes clips |
| + | *ZeroMapQual(%) - only excludes clips |
| + | *MapQual<10(%) - only excludes clips |
| + | *PairedReads(%) - only excludes clips |
| + | *ProperPaired(%) - only excludes clips |
| + | *DupRate(%) - only excludes clips |
| + | *QCFailRate(%) - only excludes clips |
| + | *AverageMapQuality - excludes unmapped reads, duplicates, failed QC, deletions/skips (only CIGAR M/X/= are included), MapQ 255 |
| + | *AverageMapQualCount - excludes unmapped reads, duplicates, failed QC, deletions/skips (only CIGAR M/X/= are included), MapQ 255 |
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| === Sample Output === | | === Sample Output === |