SAMtools-view (format conversion) Introduction:SAM file <=> BAM file. Input&Output: SAM file & BAM file Test inputs: input_sam & inpput_bam (SAM&BAM) imcas:/test_kira/SAMtools/yeast.sam imcas:/test_kira/SAMtools/yeast.bam SAMtools-sort (format conversion) Introduction:The sort command sorts a BAM file based on its position in the reference, as determined by its alignment. Input: BAM file Output: sorted BAM file Test inputs: input_bam (BAM) imcas:/test_kira/SAMtools/yeast.bam SAMtools-mpileup (variant calling) Introduction:The mpileup command produces a pileup format (or BCF) file giving, for each genomic coordinate, the overlapping read bases and indels at that position in the input BAM files(s). This can be used for SNP calling for example. Input: reference genome (in fasta format) and sorted BAM file (output file from SAMtools-sort, in bam format). Output: binary counterpart of variant call format file (in BCF format) Test inputs: input_bam (bam) imcas:/test_kira/SAMtools/yeast.sorted.bam input_reference (fas/fasta/fna/fa) imcas:/test_kira/SAMtools/GCF_000146045.2_R64_genomic.fna Test example: ?.bcf 861.10MB SAMtools-index (format conversion) Introduction:The index command creates a new index file that allows fast look-up of data in a (sorted) SAM or BAM. (Note: You must sort the bam files before you can index) Input: sorted BAM file (output file from SAMtools-sort, in bam format) Output: bai file Test inputs: input_bam (bam) imcas:/test_kira/Samtools/yeast.sorted.bam BCFtools-view (format conversion) Introduction:Convert between VCF and BCF. Calling variant candidates and estimate allele frequencies. Input: bcf file (output file from Samtools-mpileup) Output: vcf file (Variant Call Format file) Test inputs: input_bcf (bcf) /test_kira/Samtools/yeast.bcf SAMtools-flagstat (statistics) Introduction:Give the comparison result of BAM file. Input&output: BAM file & txt file Test inputs: input_bam (bam) /test_kira/SAMtools/yeast.bam Test example: ?.txt 388.00B Figure: the report of the mapping result.