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

Fixed up examples: pasting from wiki still had old rod syntax

This commit is contained in:
Guillermo del Angel 2011-08-17 16:29:45 -04:00
parent 297c9e513c
commit c193f52e5d
2 changed files with 6 additions and 6 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

10
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
View File

@ -64,11 +64,11 @@ import static java.lang.Math.log10;
* <pre>
* java -Xmx4000m -jar dist/GenomeAnalysisTK.jar \
* -R reffile.fasta -T BeagleOutputToVCF \
* -B:variant,VCF input_vcf.vcf \
* -B:beagleR2,BEAGLE /myrun.beagle_output.r2 \
* -B:beaglePhased,BEAGLE /myrun.beagle_output.phased \
* -B:beagleProbs,BEAGLE /myrun.beagle_output.gprobs \
* --out output_vcf.vcf
* -V input_vcf.vcf \
* -beagleR2:BEAGLE /myrun.beagle_output.r2 \
* -beaglePhased:BEAGLE /myrun.beagle_output.phased \
* -beagleProbs:BEAGLE /myrun.beagle_output.gprobs \
* -o output_vcf.vcf
* </pre>
<p> Note that Beagle produces some of these files compressed as .gz, so gunzip must be run on them before walker is run in order to decompress them </p>

2
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
View File

@ -68,7 +68,7 @@ import java.util.*;
* <pre>
* java -Xmx2g -jar dist/GenomeAnalysisTK.jar -L 20 \
* -R reffile.fasta -T ProduceBeagleInput \
* -B:variant,VCF path_to_input_vcf/inputvcf.vcf -o path_to_beagle_output/beagle_output
* -V path_to_input_vcf/inputvcf.vcf -o path_to_beagle_output/beagle_output
* </pre>
*
*/