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So let's recap: we have mapped reads to genome, converted them from a BWA specific format to a more
So let's recap: we have mapped reads to genome, converted them from a BWA specific format to a more
commonly used format used by many different programs, sorted and indexed the results.
commonly used format used by many different programs, sorted and indexed the results.
In most cases, the next step would be to remove duplicate reads and to ensure that base quality scores are properly calibrated. To save time, we'll skip those steps now.
Till now, we only finished read mapping for one sample SAMPLE1. We need to repeat this step for other samples (SAMPL2 - SAMPLE40).
foreach file (`ls fastq/SAMPLE*.fastq | cut -f 2 -d '/' | cut -f 1 -d '.'`)
echo $file
bin/bwa aln -q 15 ref/human_g1k_v37_chr20.fa fastq/$file.fastq > bwa.sai/$file.sai
bin/bwa samse -r "@RG\tID:ILLUMINA\tSM:$file" ref/human_g1k_v37_chr20.fa bwa.sai/$file.sai fastq/$file.fastq | \
bin/samtools view -uhS - | bin/samtools sort -m 2000000000 - bams/$file
bin/samtools index bams/$file.bam
end
== Calling variants and Inferring genotypes ==
== Calling variants and Inferring genotypes ==
