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| | | |
| <span style="color:#D2691E">ASP is a new format that is currently in production, so this tool is not yet available for public release.</span> | | <span style="color:#D2691E">ASP is a new format that is currently in production, so this tool is not yet available for public release.</span> |
| + | |
| + | |
| + | == Rules == |
| + | |
| + | '''Dealing with 'N' Bases''' |
| + | * If the reference is 'N': |
| + | ** Do Not write REF_ONLY or DETAILED records |
| + | ** Either write EMPTY or no record (depending on Gap Size and the next data record) |
| + | * If all reads at this position are 'N': |
| + | ** Either write EMPTY or no record (depending on Gap Size and the next data record) |
| + | * If some reads are 'N' and the rest are the reference (not 'N') |
| + | ** Write a REF_ONLY record but do not include the 'N's in the numBases |
| + | * If some reads are 'N' and some are non-reference (not 'N') |
| + | ** DEFAULT: Write a DETAILED record and include the 'N's in the numBases |
| + | ** OPTIONAL: Write a DETAILED record but do not include the 'N's in the numBases |
| | | |
| | | |
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| </pre> | | </pre> |
| | | |
| + | == Required Parameters == |
| {{inBAMInputFile}} | | {{inBAMInputFile}} |
| | | |
− | == output File <code>(--out)</code>== | + | === output File <code>(--out)</code>=== |
| | | |
| Use <code>--out</code> followed by your file name to specify the ASP file to write from the pileup. | | Use <code>--out</code> followed by your file name to specify the ASP file to write from the pileup. |
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| | | |
| {{RefFile}} | | {{RefFile}} |
| + | |
| + | == Optional Parameters == |
| {{BamIndex}} | | {{BamIndex}} |
| | | |
− | == Region List <code>(--regionList)</code> == | + | === Region List <code>(--regionList)</code> === |
| Use the <code>--regionList</code> option if you only want to pileup specific regions instead of the entire BAM file. The region list file has one region on each line. | | Use the <code>--regionList</code> option if you only want to pileup specific regions instead of the entire BAM file. The region list file has one region on each line. |
| | | |
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| If a position is covered by multiple regions, the position will be piled up multiple times (once for each region). | | If a position is covered by multiple regions, the position will be piled up multiple times (once for each region). |
| | | |
− | == Gap Size <code>(--gapSize)</code> == | + | === Gap Size <code>(--gapSize)</code> === |
| When writing an ASP file, there are two ways to skip positions that do not have any data (records/bases) associated with them. | | When writing an ASP file, there are two ways to skip positions that do not have any data (records/bases) associated with them. |
| # Write an Empty record indicating no data for that position. | | # Write an Empty record indicating no data for that position. |
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| {{paramsParameter}} | | {{paramsParameter}} |
| | | |
− |
| |
− | == Asp File Name <code>(--asp)</code>==
| |
− |
| |
− | Use <code>--asp</code> followed by the file name of the ASP file that you want to read.
| |
− |
| |
− | == Only print Data Records <code>(--dataOnly)</code>==
| |
− | The <code>--dataOnly</code> option tells the tool to print only Reference Only and Detailed records. Any Empty and Position records are not printed.
| |
− |
| |
− | {{paramsParameter}}
| |
| | | |
| = Return Value = | | = Return Value = |
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| | | |
| =Output= | | =Output= |
− | Each ASP record is printed on one line with each field separated by a <code>tab</code>.
| + | An [[LibStatGen: ASP|ASP]] file is written containing the pileup for the specified BAM file. ASP files are by default compressed using BGZF. |
| | | |
− | The 1st field in the row is the chromosomeID and 0-based position separated by a ':'. | + | The number of each type of record is output to stderr. |
| | | |
− | The 2nd field is the record type, <code>POS</code>, <code>EMPTY</code>, <code>REF_ONLY</code>, or <code>DETAILED</code>.
| + | For example: |
− | | + | <pre> |
− | <code>POS</code> and <code>EMPTY</code> records have no additional columns.
| + | Number of Position Records = 6 |
− | | + | Number of Empty Records = 39 |
− | <code>REF_ONLY</code> records have 3 additional fields: | + | Number of Reference Only Records = 12 |
− | # numBases - the number of bases at this position
| + | Number of Detailed Records = 29 |
− | # GLH - the GLH for this position
| + | </pre> |
− | # GLA - the GLA for this position
| |
− | | |
− | <code>DETAILED</code> records have 6 additional fields:
| |
− | # numBases - the number of bases at this position
| |
− | # bases - the bases at this position. String of ACTGND characters that is numBases long. ('D' represents a deletion)
| |
− | # qualities - the qualities at this position. String of characters representing the qualities that is numBases long. (' ' represents the quality of a deletion)
| |
− | # cycles - the cycles for this position. There are numBases cycles, separated by a ':'. (-1 represents the cycle of a deletion)
| |
− | # strands - the strands for this position. Sequence of numBases 0's and 1's. 0 represents forward strand and 1 represents reverse strand.
| |
− | # mqs - the mapping qualities for this position. There are numBases mapping qualities, separated by a ':'.
| |
− | | |
− | ==Sample Output==
| |