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And now the DOCS! 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2729 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2010-01-28 23:21:33 +00:00
parent 40262e2070
commit 4810e9c9cd
1 changed files with 16 additions and 13 deletions
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29
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java
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@ -19,11 +19,14 @@ import net.sf.samtools.CigarOperator;
import net.sf.samtools.CigarElement;
/**
* Created by IntelliJ IDEA.
* User: asivache
* Date: Oct 15, 2009
* Time: 2:03:03 PM
* To change this template use File | Settings | File Templates.
* This is a simple, counts-and-cutoffs based tool for calling indels from aligned (preferrably MSA cleaned) sequencing
* data. Two output formats supported are: BED format (minimal output, required), and extended output that includes read
* and mismtach statistics around the calls (tuned on with --verbose). The calls can be performed from a single/pooled sample,
* or from a matched pair of samples (with --somatic option). In the latter case, two input bam files must be specified,
* the order is important: indels are called from the second sample ("Tumor") and additionally annotated as germline
* if even a weak evidence for the same indel, not necessarily a confident call, exists in the first sample ("Normal"), or as somatic
* if first bam has coverage at the site but no indication for an indel. In the --somatic mode, BED output contains
* only somatic calls, while --verbose output contains all calls annotated with GERMLINE/SOMATIC keywords.
*/
@ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class, PlatformUnitFilter.class})
public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
@ -32,23 +35,23 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
@Argument(fullName="1kg_format", shortName="1kg", doc="output in 1000 genomes format", required=false)
boolean FORMAT_1KG = false;
@Argument(fullName="somatic", shortName="somatic",
doc="Perform somatic calls; two input alignment files must be specified", required=false)
doc="Perform somatic calls; two input alignment files (-I option) must be specified. Calls are performed from the second file (\"tumor\") against the first one (\"normal\").", required=false)
boolean call_somatic = false;
@Argument(fullName="verbose", shortName="verbose",
doc="Tell us what you are calling now (printed to stdout)", required=false)
doc="Prints all calls (both germline and somatic if --somatic is used) with additional read/mismatch statistics into GATK output stream (redirect with -o).", required=false)
boolean verbose = false;
@Argument(fullName="minCoverage", shortName="minCoverage",
doc="must have minCoverage or more reads to call indel; with --somatic this value is applied to tumor sample", required=false)
doc="indel calls will be made only at sites with coverage of minCoverage or more reads; with --somatic this value is applied to tumor sample", required=false)
int minCoverage = 6;
@Argument(fullName="minNormalCoverage", shortName="minNormalCoverage",
doc="used only with --somatic; normal sample must have at least minNormalCoverage or more reads to call germline/somatic indel", required=false)
doc="used only with --somatic; normal sample must have at least minNormalCoverage or more reads at the site to call germline/somatic indel, otherwise the indel (in tumor) is ignored", required=false)
int minNormalCoverage = 4;
@Argument(fullName="minFraction", shortName="minFraction",
doc="Minimum fraction of reads with CONSENSUS indel at a site, out of all reads covering the site, required for a consensus call"+
doc="Minimum fraction of reads with CONSENSUS indel at a site, out of all reads covering the site, required for making a call"+
" (fraction of non-consensus indels at the site is not considered here, see minConsensusFraction)", required=false)
double minFraction = 0.3;
@Argument(fullName="minConsensusFraction", shortName="minConsensusFraction",
doc="Minimum fraction of CONSENSUS indel observations at a site wrt all indel observations at the site required to make the call", required=false)
doc="Indel call is made only if fraction of CONSENSUS indel observations at a site wrt all indel observations at the site exceeds this threshold", required=false)
double minConsensusFraction = 0.7;
@Argument(fullName="minIndelCount", shortName="minCnt",
doc="Minimum count of reads supporting consensus indel required for making the call. "+
@ -56,13 +59,13 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
"(minIndelCount not met) will not pass.", required=false)
int minIndelCount = 0;
@Argument(fullName="refseq", shortName="refseq",
doc="Name of RefSeq transcript annotation file. If specified, indels will be annotated as GENOMIC/UTR/INTRON/CODING", required=false)
doc="Name of RefSeq transcript annotation file. If specified, indels will be annotated with GENOMIC/UTR/INTRON/CODING and with the gene name", required=false)
String RefseqFileName = null;
@Argument(fullName="blacklistedLanes", shortName="BL",
doc="Name of lanes (platform units) that should be ignored. Reads coming from these lanes will never be seen "+
"by this application, so they will not contribute indels to consider and will not be counted.", required=false)
PlatformUnitFilterHelper dummy;
@Argument(fullName="indel_debug", shortName="idebug", doc="Detailed printout for debugging",required=false) Boolean DEBUG = false;
@Argument(fullName="indel_debug", shortName="idebug", doc="Detailed printout for debugging, do not turn this on",required=false) Boolean DEBUG = false;
@Argument(fullName="window_size", shortName="ws", doc="Size (bp) of the sliding window used for accumulating the coverage. "+
"May need to be increased to accomodate longer reads or longer deletions.",required=false) int WINDOW_SIZE = 200;