Samtools
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| title | mkdir -p 03_Output/variant_calling/samtools |
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If you do not have a alignment file in the SAM format you may want to start with Introduction to mapping.
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| title | cp 03_Output/mapping/bowtie/REL606.5.sam 03_Output/variant_calling/samtools/ |
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| title | cp 03_Output/mapping/bowtie/REL606.5.fasta 03_Output/variant_calling/samtools/ |
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| borderStyle | solid |
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Prepare reference file.
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| title | samtools faidx 03_Output/variant_calling/samtools/REL606.5.fasta |
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| borderStyle | solid |
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Prepare alignment file.
Convert SAM to BAM format.
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| title | samtools view -bS -o 03_Output/variant_calling/samtools/REL606.5.bam 03_Output/mapping/bowtie/REL606.5.sam |
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| borderStyle | solid |
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[bam_header_readsamopen] EOFSAM markerheader is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[main_samview] fail to read the header from "03_Output/mapping/bowtie/REL606.5.sam" present: 1 sequences.
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Variant call output.
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| 1 | bcftools view -vcg - > 03_Output/variant_calling/samtools/output.vcf |
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| title | samtools mpileup -uf 03_Output/variant_calling/samtools/REL606.5.fasta 03_Output/variant_calling/samtools/REL606.5.bam |
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[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
[bam_pileup_core] the input is not sorted (reads out of order)
[afs] 0:0.000 1:0.000 2:0.000
[bam_plp_destroy] memory leak: 1. Continue anyway.
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