samtools index aln-pe.mapped.sorted.bam
for i in $(samtools view -H aln-pe.mapped.sorted.bam | awk -F"\t" '/@SQ/{gsub("^SN:","",$2);print $2}'
); do samtools view -b aln-pe.mapped.sorted.bam $i > aln-pe.mapped.sorted.$i.bam; java -Xmx2g -jar $(which CollectGcBiasMetrics.jar) R=data/Cdiff078.fa I=aln-pe.mapped.sorted.$i.bam O=aln-pe.mapped.sorted.${i}_GCBias.txt CHART=aln-pe.mapped.sorted.${i}_GCBias.pdf ASSUME_SORTED=true; done
