533
edits
Changes
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foreach file (`ls fastq/SAMPLE*.fastq | cut -f 2 -d '/' | cut -f 1 -d '.'`)
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/$file
bin/samtools view -uhS - | bin/samtools sort -m 2000000000 - bams/$file
bin/samtools index bams/$file.bam
end
end
== Calling variants and Inferring genotypes ==
== Calling variants and Inferring genotypes ==
