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Expand title What new files were created by these commands? Code Block language bash title List the contents of the output directory ls samtools_bowtie2
Code Block title Expected output NC_012967.1.fasta SRR030257.sorted.bam.bai NC_012967.1.fasta.fai SRR030257.sam SRR030257.bam SRR030257.sorted.bam
Expand title Why didn't we name the output SRR030257.sorted.bam in the samtools sort command? Samtools appends an extra .bam to whatever we put here, so it would have created SRR030257.sorted.bam.bam, and then we would have had to make a joke about the Flintstones.
Expand title Can you guess what a *.bai file is? Sure enough, it's the index file for the BAM file.
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mkdir comparison cp -ni samtools_bowtie2/SRR030257.vcf comparison/bowtie2.vcf cp -ni samtools_bwa/SRR030257.vcf comparison/bwa.vcf cp -ni samtools_bowtie/SRR030257.vcf comparison/bowtie.vcf cd comparison |
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- Look at how the reads supporting these variants were aligned to the reference genome in theĀ Integrative Genomics Viewer (IGV) tutorial.
- Look into more sophisticated variant calling with GATK. We recommend starting from theĀ GATK best practice page.