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| Code Block |
|---|
cp bowtie/REL606.5.sam samtools/ cp bowtie/REL606.5.fasta samtools/ |
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Index reference file.
| Code Block | |
|---|---|
| title | samtools faidx samtools/REL606.5.fasta |
| borderStyle | solid |
Prepare alignment file.
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Convert SAM to BAM format.
| Code Block | ||||
|---|---|---|---|---|
| title | samtools view -bS -o samtools/REL606.5.bam bowtie/REL606.5.sam | |borderStyle | solid | [samopen] SAM header is present: 1 sequences.=solid} |
Sort BAM file.
| Code Block | |
|---|---|
| title | samtools sort samtools/REL606.5.bam samtools/sorted_REL606.5 |
| borderStyle | solid |
[bam_sort_core] merging from 2 files...
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Variant call output.
| Code Block | |
|---|---|
| 1 | bcftools view -vcg - > samtools/output.vcf | title | samtools mpileup -ufsamtools mpileup -uf samtools/REL606.5.fasta samtools/sorted_REL606.5.bam |
| borderStyle | solid | [mpileup] 1 samples in 1 input files <mpileup> Set max per-file depth to 8000 [bcfview] 100000 sites processed. [afs] 0:99910.349 1:52.764 2:36.886 [bcfview] 200000 sites processed. [afs] 0:99946.543 1:48.457 2:5.000 [bcfview] 300000 sites processed. [afs] 0:99976.591 1:5.410 2:17.999 [bcfview] 400000 sites processed. [afs] 0:99984.243 1:8.357 2:7.399 [bcfview] 500000 sites processed. [afs] 0:99970.803 1:23.197 2:6.000 [afs] 0:63952.773 1:6.227 2:2.000 \|bcftools view -vcg - \> samtools/output.vcf |
Produces output.vcf from Bowtie and output.vcf from BWA.
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