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Fixed docs for Pileup walker

This commit is contained in:
Eric Banks 2012-09-05 09:55:34 -04:00
parent d795437202
commit fc06f39411
1 changed files with 2 additions and 13 deletions
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15
public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java
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@ -45,19 +45,8 @@ import java.util.Collections;
import java.util.List;
/**
* Prints the alignment in the pileup format. In the pileup format, each line represents a genomic position,
* consisting of chromosome name, coordinate, reference base, read bases, read qualities and alignment mapping
* qualities. Information on match, mismatch, indel, strand, mapping quality and start and end of a read are all
* encoded at the read base column. At this column, a dot stands for a match to the reference base on the forward strand,
* a comma for a match on the reverse strand, 'ACGTN' for a mismatch on the forward strand and 'acgtn' for a mismatch on the
* reverse strand.
*
* A pattern '\+[0-9]+[ACGTNacgtn]+' indicates there is an insertion between this reference position and the next
* reference position. The length of the insertion is given by the integer in the pattern, followed by the inserted sequence.
* Similarly, a pattern '-[0-9]+[ACGTNacgtn]+' represents a deletion from the reference.
* Also at the read base column, a symbol '^' marks the start of a read segment which is a contiguous subsequence on the read
* separated by 'N/S/H' CIGAR operations. The ASCII of the character following '^' minus 33 gives the mapping quality.
* A symbol '$' marks the end of a read segment.
* Prints the alignment in something similar to the samtools pileup format. Each line represents a genomic position,
* consisting of chromosome name, coordinate, reference base, read bases, and read qualities.
*
* Associated command:
* samtools pileup [-f in.ref.fasta] [-t in.ref_list] [-l in.site_list] [-iscg] [-T theta] [-N nHap] [-r pairDiffRate] <in.alignment>