zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

docs updated

This commit is contained in:
Andrey Sivachenko 2012-03-07 18:47:15 -05:00
parent 117ea605ac
commit 56f074b520
1 changed files with 11 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

12
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
View File

@ -75,7 +75,7 @@ import java.util.*;
* <p>
* This is a simple, counts-and-cutoffs based tool for calling indels from aligned (preferrably MSA cleaned) sequencing
* data. Supported output formats are: BED format, extended verbose output (tab separated), and VCF. The latter two outputs
* include additional statistics such as mismtaches and base qualitites around the calls, read strandness (how many
* include additional statistics such as mismatches and base qualitites around the calls, read strandness (how many
* forward/reverse reads support ref and indel alleles) etc. It is highly recommended to use these additional
* statistics to perform post-filtering of the calls as the tool is tuned for sensitivity (in other words it will
* attempt to "call" anything remotely reasonable based only on read counts and will generate all the additional
@ -92,6 +92,16 @@ import java.util.*;
* bam tagging is not required in this case, and tags are completely ignored if still used: all input bams will be merged
* on the fly and assumed to represent a single sample - this tool does not check for sample id in the read groups).
*
* Which (putative) calls will make it into the output file(s) is controlled by an expression/list of expressions passed with -filter
* flag: if any of the expressions evaluate to TRUE, the site will be discarded. Otherwise the putative call and all the
* associated statistics will be printed into the output. Expressions recognize the following variables(in paired-sample
* somatic mode variables are prefixed with T_ and N_ for Tumor and Normal, e.g. N_COV and T_COV are defined instead of COV):
* COV for coverage at the site, INDEL_F for fraction of reads supporting consensus indel at the site (wrt total coverage),
* INDEL_CF for fraction of reads with consensus indel wrt all reads with an indel at the site, CONS_CNT for the count of
* reads supporting the consensus indel at the site. Conventional arithmetic and logical operations are supported. For instance,
* N_COV<4||T_COV<6||T_INDEL_F<0.3||T_INDEL_CF<0.7 instructs the tool to only output indel calls with at least 30% observed
* allelic fraction and with consensus indel making at least 70% of all indel observations at the site, and only at the sites
* where tumor coverage and normal coverage are at least 6 and 4, respectively.
* <h2>Input</h2>
* <p>
* Tumor and normal bam files (or single sample bam file(s) in --unpaired mode).