Exome II: QC, filtering and mapping

Course: HT17 Bioinformatics in Genomics (SC00024)

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Due to limit in time, we will be working with chr11. The control sample has already been analyzed from top to toe, while the patient sample was only mapped. You will be in charge of running the last steps of the analysis for the patient sample.

The data was trimmed using $trim_galore (DON'T RUN!):

time $trim_galore -q 20 --phred33 --fastqc --gzip --length 20 \
--paired Fastq/AS_2.chr11.R1.fastq.gz Fastq/AS_2.chr11.R2.fastq.gz  

Q. How does the quality look like, before and after trimming? How many reads were trimmed for both the control and the patient sample?

Then, the trimmed data was mapped towards $chr11_ref using bwa mem (DON'T RUN!):

time bwa mem $chr11_ref \
TrimGalore/AS_2.chr11.R1_val_1.fq.gz TrimGalore/AS_2.chr11.R2_val_2.fq.gz | \
samtools view -Sb -o Alignment/AS_2.bwa.bam - &

Metadata was added with $picard and then sorted and indexed with samtools (DON'T RUN!).

time samtools sort -o Alignment/AS_2.bwa.sort.bam Alignment/AS_2.bwa.bam 

time java -jar $picard AddOrReplaceReadGroups \
   I=Alignment/AS_2.bwa.sort.bam \
   O=Alignment/AS_2.bwa.sort.fix.bam \
   SO=coordinate \
   RGID=AS_2 \
   RGLB=AS_2 \
   RGPL=Illumina \
   RGPU=AS_2 \
   RGSM=AS_2 & 

samtools index Alignment/AS_2.bwa.sort.fix.bam

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Next: Exome III: Alignment processing and variant discovery

Previous: Exome I: Intro

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Created by Marcela Dávila