Hi, I wonder what should I do to obtain a dataset to draw a plot showing GC content against mean depth for exome data (like this). I have bam files, bed files, fastQ files but I don't even know where I should start.
Thanks
1 answer
So I have done the following :
Using
bedtool nucI have calculated the GC content of each region of my bed fileUsing samtools bedcov, I have calculated the average depth of coverage for each region of my bed :
samtools bedcov -Q 30 Intervals.bed sample.bam | sort -k1,1 -k2,2n -k3,3n | awk 'BEGIN {OFS="\t"}{a=($3-$2+1);b=($5/a);print $1,$2,$3,$4,b,"+","+"}' > sample_coverage.tsvUsing bedtools intersect or a simple join you can have the data to draw a plot depth ov coverage Versus GC content (%)
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Is CollectGcBiasMetrics (Picard) what I am looking for ?
see Plot Coverage Vs. Gc Content for a start