Question

Exome data : drawing a plot showing GC content against normalized mean

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5.5 years ago

pegeot.henri • 0

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

exome GC content • 1.5k views

ADD COMMENT • link 5.5 years ago by pegeot.henri • 0

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see Plot Coverage Vs. Gc Content for a start

ADD REPLY • link 5.5 years ago by Pierre Lindenbaum 164k

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Is CollectGcBiasMetrics (Picard) what I am looking for ?

ADD REPLY • link 5.5 years ago by pegeot.henri • 0

score 0 · Answer 1 · 2019-05-17

So I have done the following :

Using bedtool nuc I have calculated the GC content of each region of my bed file
Using 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.tsv
Using bedtools intersect or a simple join you can have the data to draw a plot depth ov coverage Versus GC content (%)