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Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Matt Hanna 2011-08-17 16:59:12 -04:00
parent 81a792afeb c193f52e5d
commit c104dd7a09
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>
* 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
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@ -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>
*
*/