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10 December 2020, 08:13:14 UTC
Revision d64c7115b852e3a269ed9e3c069a3485b34bbea5 authored by Eric Sanford on 10 October 2019, 18:04:36 UTC, committed by Eric Sanford on 10 October 2019, 18:04:36 UTC
added location of hg19 reference files as comments to setEnvironmentVariables.sh script
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Tip revision: d64c7115b852e3a269ed9e3c069a3485b34bbea5 authored by Eric Sanford on 10 October 2019, 18:04:36 UTC
added location of hg19 reference files as comments to setEnvironmentVariables.sh script
Tip revision: d64c711
samToSortedBam.sh 
#!
# run from within "repo" directory

EXPERIMENT=$1
SAMPLEID=$2

ALIGNMENT_TOOL_NAME=bowtie2

if [[ ! -z "$3" ]]; then
    ALIGNMENT_TOOL_NAME="$3"
fi

COMMANDNAME=samtools

if [ ! -d $EXPERIMENT/analyzed/$SAMPLEID/log ]; then
    mkdir $EXPERIMENT/analyzed/$SAMPLEID/log
fi

JOURNAL=$EXPERIMENT/analyzed/$SAMPLEID/log/$(date +%Y-%m-%d_%H-%M).$COMMANDNAME.log

COMMAND="samtools view -bS \
    $EXPERIMENT/analyzed/$SAMPLEID/$ALIGNMENT_TOOL_NAME/$SAMPLEID.Aligned.out.sam \
    | samtools sort - \
    $EXPERIMENT/analyzed/$SAMPLEID/$ALIGNMENT_TOOL_NAME/$SAMPLEID.sorted"


INDEXCOMMAND="samtools index \
    $EXPERIMENT/analyzed/$SAMPLEID/$ALIGNMENT_TOOL_NAME/$SAMPLEID.sorted.bam \
    $EXPERIMENT/analyzed/$SAMPLEID/$ALIGNMENT_TOOL_NAME/$SAMPLEID.sorted.bai"

REMOVE_SAM_COMMAND="rm $EXPERIMENT/analyzed/$SAMPLEID/$ALIGNMENT_TOOL_NAME/$SAMPLEID.Aligned.out.sam"

echo "Starting..." >> $JOURNAL

date >> $JOURNAL
echo $COMMAND >> $JOURNAL
eval $COMMAND

date >> $JOURNAL
echo $INDEXCOMMAND >> $JOURNAL
eval $INDEXCOMMAND

date >> $JOURNAL
echo $REMOVE_SAM_COMMAND >> $JOURNAL
eval $REMOVE_SAM_COMMAND

date >> $JOURNAL
echo "Done" >> $JOURNAL