Qualimap whole exome sequencing depth of coverage - use whole genome or exome as reference?
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5 weeks ago
rebeliscu ▴ 30

I'm trying to calculate the depth of coverage from my WXS data.

Using Qualimap, I first used as the feature file the Gencode human genome (release 38) .gtf file associated with the genome I aligned to:

feat="gencode.v38.primary_assembly.annotation.gtf"
for ea in *bam
  do $qualimap bamqc \
  --java-mem-size=20G \
  -bam $ea \
  --feature-file $feat
done;

... and the coverage was ~6.8.

I then subset the .gtf file to exonic regions only:

grep 'transcript_type "protein_coding"' gencode.v38.primary_assembly.annotation.gtf |
awk '($3=="exon") {printf("%s\t%s\t%s\n",$1,int($4)-1,$5);}' |
sort -T . -k1,1 -k2,2n |
bedtools merge |
awk 'BEGIN{OFS="\t"}{print $1,$2,$3,$4,0,"."}' \
> gencode.v38.primary_assembly.annotation_exome.bed

feat="gencode.v38.primary_assembly.annotation_exome.bed"
for ea in *bam
  do $qualimap bamqc \
  -bam $ea \
  --feature-file $feat
done;

...and the coverage jumped to ~68.

Is the latter the correct coverage given that my target is the human exome?

Thanks in advance.

coverage wxs qualimap depth • 129 views
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