S8-variant-coverage

S8 Pipeline - Coverage of variants from a bam file

Author: Philippe Sanio

The S8 pipeline maps the mean coverage of a sequence.bam file to a given variants.vcf file. For the extraction of the coverage Mosdepth is bing used.

Pipeline

• Inputs
  • sequence.bam
  • variants.vcf
• Output:
  • plots with the coverage mapped to the variant call.

Mosdepth

For the coverage extraction mosdepth is being used. In this example the coverage is being calculated for each basepair (bp), the binsize of 10bp and a quality of above 20. The output will be used for S8 pipeline.

mosdepth -n -b 1 -t 12 -Q 20 ./coverage ./sequence.bam

The option -x (dont look at internal cigar operations) is not activated to ensure counting coverage for indels.

S8

The S8 pipeline maps the mean coverage for each variant in the .vcf file and outputs a plot for each varient type

python s8 coverage.per-base.bed.gz variants.vcf

Results

Sample 1: HG002 GRCh38

• Bam: HG002.hiseqx.pcr-free.40x.dedup.grch38.bam
  • https://storage.googleapis.com/brain-genomics-public/research/sequencing/grch38/bam/hiseqx/wgs_pcr_free/40x/HG002.hiseqx.pcr-free.40x.dedup.grch38.bam
• VCF: HG002.hiseqx.pcr-free.40x.deepvariant-v1.0.grch38.vcf.gz
  • https://storage.googleapis.com/brain-genomics-public/research/sequencing/grch38/vcf/hiseqx/wgs_pcr_free/40x/HG002.hiseqx.pcr-free.40x.deepvariant-v1.0.grch38.vcf.gz

Results for sample HG002-GRCh38-Hiseqx-40X: Chr 1,6 and 18: