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

Deleting old shell code 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4962 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-01-07 21:36:16 +00:00
parent e64a300642
commit be67161b47
5 changed files with 2 additions and 81 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
shell/buildRODs.sh
View File

@ -1,2 +0,0 @@
java -Xmx40000m -cp ../java/dist/AnalysisTK.jar org.broadinstitute.sting.atk.PrepareROD REF_FILE_ARG=/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta ROD_FILE=/seq/references/dbsnp/downloads/snp129_hg18.txt OUT=`echo $1/snp129_hg18.txt.rod` ROD_TYPE=dbSNP ROD_NAME=dbSNP

9
shell/calcCallerMD5s.csh
View File

@ -1,9 +0,0 @@
#!/bin/tcsh
foreach model (ONE_STATE THREE_STATE EMPIRICAL)
java -Xmx4096m -jar ~/dev/GenomeAnalysisTK/trunk/dist/GenomeAnalysisTK.jar -l INFO -L 1:10,000,000-11,000,000 -R /broad/1KG/reference/human_b36_both.fasta -T SingleSampleGenotyper -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout ./$model.geli.calls -lod 5 -m $model
end
wc -l *.geli.calls
md5sum *.geli.calls

2
shell/makeResources.sh
View File

@ -1,2 +0,0 @@
cd dist/packages/GATKResources
tar cvhzf gatk_resources_062309.tgz resources

66
shell/readStatsDiff.sh
View File

@ -1,66 +0,0 @@
#!/usr/bin/csh
# ##############################################################################
# this file can be used to diff the flagstat values for a whole genome,
# along with sub-diffs for each chromosome. This may be helpful if you're
# debugging a specific reads problem, and you want to know the differences
# between the output of the GATK and samtools
# ##############################################################################
if ($#argv != 3) then
echo "usage readStatsDiff <bamfile.bam> <referenceSequence.fasta> <outputFile>"; exit 1
endif
if (! -f $1) then
echo bam file $2 does not seem to exist; exit 1
endif
if (! -f $2) then
echo reference file $2 does not seem to exist; exit 1
endif
if ( -e $3) then
echo output file $3 already exists!; exit 1
endif
# set the bam and the reference index
set bam = $1
set seq = $2
set out = $3
# diff the whole chromosome
java -ea -Xmx4096m \
-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=8015 \
-jar dist/GenomeAnalysisTK.jar \
-S SILENT \
-T FlagStatRead \
-I $bam \
-R $seq \
-oe 1.out
samtools flagstat $bam > 2.out
echo "\n" >> $out
echo results for whole bam file >> $out
echo "\n" >> $out
diff 1.out 2.out >> $out
rm 1.out
rm 2.out
foreach chromosome (chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX)
java -ea -Xmx4096m \
-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=8015 \
-jar dist/GenomeAnalysisTK.jar \
-S SILENT \
-T FlagStatRead \
-I $bam \
-R $seq \
-oe 1.out \
-L $chromosome
samtools view -h -b $bam $chromosome > temp.bam
samtools flagstat temp.bam > 2.out
echo results for $chromosome >> $out
echo "\n" >> $out
diff 1.out 2.out >> $out
rm temp.bam
rm 1.out
rm 2.out
end

4
shell/syncWithDevOnGSA2.csh
View File

@ -1,6 +1,6 @@
#!/bin/tcsh
setenv HERE java
setenv HERE "java tribble"
setenv THERE \~/dev/GenomeAnalysisTKFromLaptop/trunk
rsync -e ssh -aCvz $HERE depristo@gsa2:$THERE
rsync -e ssh -aCvz $HERE depristo@gsa1:$THERE