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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
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10
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
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@ -64,11 +64,11 @@ import static java.lang.Math.log10;
* <pre> * <pre>
* java -Xmx4000m -jar dist/GenomeAnalysisTK.jar \ * java -Xmx4000m -jar dist/GenomeAnalysisTK.jar \
* -R reffile.fasta -T BeagleOutputToVCF \ * -R reffile.fasta -T BeagleOutputToVCF \
* -B:variant,VCF input_vcf.vcf \ * -V input_vcf.vcf \
* -B:beagleR2,BEAGLE /myrun.beagle_output.r2 \ * -beagleR2:BEAGLE /myrun.beagle_output.r2 \
* -B:beaglePhased,BEAGLE /myrun.beagle_output.phased \ * -beaglePhased:BEAGLE /myrun.beagle_output.phased \
* -B:beagleProbs,BEAGLE /myrun.beagle_output.gprobs \ * -beagleProbs:BEAGLE /myrun.beagle_output.gprobs \
* --out output_vcf.vcf * -o output_vcf.vcf
* </pre> * </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> <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
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@ -68,7 +68,7 @@ import java.util.*;
* <pre> * <pre>
* java -Xmx2g -jar dist/GenomeAnalysisTK.jar -L 20 \ * java -Xmx2g -jar dist/GenomeAnalysisTK.jar -L 20 \
* -R reffile.fasta -T ProduceBeagleInput \ * -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> * </pre>
* *
*/ */