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Revision as of 01:32, 20 June 2014
, 01:32, 20 June 2014→Setup
export CHR20_OUT=~/personal/output.20
export CHR20_OUT=~/personal/output.20
mkdir -p $CHR20_OUT
mkdir -p $CHR20_OUT
export EXOME_OUT=~/personal/output.exome
mkdir -p $EXOME_OUT
ALIGN_OUT needs to point to where your alignment output went, so if your output is not ~/personal/output, please set OUT appropriately
ALIGN_OUT needs to point to where your alignment output went, so if your output is not ~/personal/output, please set OUT appropriately
Verify that this does not give an error:
Verify that this does not give an error:
ls $ALIGN_OUT/bams/${SAMPLE}.recal.bam
ls $ALIGN_OUT/bams/${SAMPLE}.recal.bam
== Chromosome 20 ==
== Chromosome 20 ==
