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Fix check for coordinate sorted bam #4

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Fix check for coordinate sorted bam #4

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2 changes: 1 addition & 1 deletion run_varscan
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Original file line number Diff line number Diff line change
Expand Up @@ -131,7 +131,7 @@ fi

# Check that the bam files are sorted
issort(){
didsort=$(samtools view -H $1 | grep ^@HD | cut -f3)
didsort=$(samtools view -H $1 | grep -o 'SO:coordinate')
if [[ "$didsort" != 'SO:coordinate' ]]; then
graceful_death "it looks like $1 is not sorted by coordinate, please run samtools sort"
fi
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