https://bioinformaticsonline.com/snippets/view/38171/collectgcbiasmetricsjar-will-generate-a-gc-bias-plot-for-each-contig? https://bioinformaticsonline.com/snippets/view/38171/collectgcbiasmetricsjar-will-generate-a-gc-bias-plot-for-each-contig Fri, 09 Nov 2018 13:37:28 -0600 https://bioinformaticsonline.com/snippets/view/38171/collectgcbiasmetricsjar-will-generate-a-gc-bias-plot-for-each-contig 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]]> Neel