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Rev Picard to get new PF_INDEL_RATE metric. Rev preQC generator script 

to incorporate PF_INDEL_RATE.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5998 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2011-06-14 17:43:43 +00:00
parent 5be4f31515
commit 14d7ee073b
9 changed files with 12 additions and 12 deletions
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10
python/generate_per_sample_metrics.py
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@ -3,7 +3,7 @@
#
# To run:
# /humgen/gsa-hpprojects/software/bin/jython2.5.2/jython \
# -J-classpath $STING_HOME/dist/sam-1.44.794.jar:$STING_HOME/dist/picard-1.44.794.jar:$STING_HOME/dist/picard-private-parts-1859.jar \
# -J-classpath $STING_HOME/dist/sam-1.47.869.jar:$STING_HOME/dist/picard-1.47.869.jar:$STING_HOME/dist/picard-private-parts-1941.jar \
# $STING_HOME/python/generate_per_sample_metrics.py <bam.list> > <output_metrics_file.tsv>
#
# To add a new metric:
@ -45,7 +45,7 @@ bam_list_filename = sys.argv[1]
header = ['sample','HAPLOTYPES_CONFIDENTLY_MATCHING.MIN','HAPLOTYPES_CONFIDENTLY_MATCHING.MAX','HAPLOTYPES_CONFIDENTLY_MATCHING.MEDIAN',
'BAIT_SET','GENOME_SIZE','PCT_SELECTED_BASES','MEAN_TARGET_COVERAGE','ZERO_CVG_TARGETS_PCT','FOLD_80_BASE_PENALTY','PCT_TARGET_BASES_2X',
'PCT_TARGET_BASES_10X','PCT_TARGET_BASES_20X','PCT_TARGET_BASES_30X','HS_LIBRARY_SIZE','PCT_PF_READS_ALIGNED','PF_HQ_ERROR_RATE',
'MEAN_READ_LENGTH','BAD_CYCLES','STRAND_BALANCE','PCT_CHIMERAS','PCT_ADAPTER','MEDIAN_INSERT_SIZE','TOTAL_SNPS']
'PF_INDEL_RATE','MEAN_READ_LENGTH','BAD_CYCLES','STRAND_BALANCE','PCT_CHIMERAS','PCT_ADAPTER','MEDIAN_INSERT_SIZE','TOTAL_SNPS']
data = ['%s'] * len(header)
print string.join(header,'\t')
@ -88,6 +88,6 @@ for sample_id,filename in samples.items():
hybrid_selection_metrics.MEAN_TARGET_COVERAGE,hybrid_selection_metrics.ZERO_CVG_TARGETS_PCT,hybrid_selection_metrics.FOLD_80_BASE_PENALTY,
hybrid_selection_metrics.PCT_TARGET_BASES_2X,hybrid_selection_metrics.PCT_TARGET_BASES_10X,hybrid_selection_metrics.PCT_TARGET_BASES_20X,
hybrid_selection_metrics.PCT_TARGET_BASES_30X,hybrid_selection_metrics.HS_LIBRARY_SIZE,alignment_summary_metrics.PCT_PF_READS_ALIGNED,
alignment_summary_metrics.PF_HQ_ERROR_RATE,alignment_summary_metrics.MEAN_READ_LENGTH,alignment_summary_metrics.BAD_CYCLES,
alignment_summary_metrics.STRAND_BALANCE,alignment_summary_metrics.PCT_CHIMERAS,alignment_summary_metrics.PCT_ADAPTER,
insert_size_metrics.MEDIAN_INSERT_SIZE,dbsnp_matches.TOTAL_SNPS)
alignment_summary_metrics.PF_HQ_ERROR_RATE,alignment_summary_metrics.PF_INDEL_RATE,alignment_summary_metrics.MEAN_READ_LENGTH,
alignment_summary_metrics.BAD_CYCLES,alignment_summary_metrics.STRAND_BALANCE,alignment_summary_metrics.PCT_CHIMERAS,
alignment_summary_metrics.PCT_ADAPTER,insert_size_metrics.MEDIAN_INSERT_SIZE,dbsnp_matches.TOTAL_SNPS)

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settings/repository/edu.mit.broad/picard-private-parts-1859.jar → settings/repository/edu.mit.broad/picard-private-parts-1941.jar
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settings/repository/edu.mit.broad/picard-private-parts-1859.xml → settings/repository/edu.mit.broad/picard-private-parts-1941.xml
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@ -1,3 +1,3 @@
<ivy-module version="1.0">
<info organisation="edu.mit.broad" module="picard-private-parts" revision="1859" status="integration" publication="20110427114200" />
<info organisation="edu.mit.broad" module="picard-private-parts" revision="1941" status="integration" publication="20110614114100" />
</ivy-module>

3
settings/repository/net.sf/picard-1.44.794.xml
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@ -1,3 +0,0 @@
<ivy-module version="1.0">
<info organisation="net.sf" module="picard" revision="1.44.794" status="release" />
</ivy-module>

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settings/repository/net.sf/picard-1.44.794.jar → settings/repository/net.sf/picard-1.47.869.jar
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settings/repository/net.sf/picard-1.47.869.xml 100644
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@ -0,0 +1,3 @@
<ivy-module version="1.0">
<info organisation="net.sf" module="picard" revision="1.47.869" status="release" />
</ivy-module>

3
settings/repository/net.sf/sam-1.44.794.xml
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@ -1,3 +0,0 @@
<ivy-module version="1.0">
<info organisation="net.sf" module="sam" revision="1.44.794" status="release" />
</ivy-module>

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settings/repository/net.sf/sam-1.44.794.jar → settings/repository/net.sf/sam-1.47.869.jar
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settings/repository/net.sf/sam-1.47.869.xml 100644
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@ -0,0 +1,3 @@
<ivy-module version="1.0">
<info organisation="net.sf" module="sam" revision="1.47.869" status="release" />
</ivy-module>